Puella Magi Madoka Magica/WMG/3

"Deny the obvious. Uphold the inane."

The page has grown big enough to start corrupting the wiki software. Confirmed and Jossed theories are here. Unconfirmed theories are here.

Crossover Theories
"Madoka is really set in the X universe", "QB is dealing with X villain", etc etc. Just for Fun.

When Madoka turned into Hope, she turn intoThe Hope
Did anyone watch the second movie of CCS? Originally, The Nothing card had a sad face on it; a crystal-ball shout-out to PMMM's opening where Madoka sheds tears?

The Kyuubey are a branch of Auditors.
Entities who keep the stars burning and the planets orbiting; but a dim outlook on sentience. The events of Thief of Time wiped most of the old ones out; even the ones who "survived" were infected by the emotions that their human avatars accrued and went too insane to keep the universe running. The next batch learned from their predecessors mistakes and learned how to use emotion in their favor without succumbing to it; as well as created an emplated host body that did not have biological urges. The event with their predecessors also left them with a distinct opposition to Death/entropy.

Soul Gem technology is based on Philosopher's Stones
When you can condense the souls of people in order to violate Equivalent Exchange.....
 * The Incubators might have been a race that mastered alchemy, to the point that they can make a Philosopher's Stone out of a single being that still retains its sapience and strengthens itself with either its own emotions (as a Puella Magi) or sacrificing other people's souls (as a Witch).

In one of the alternate timelines, Madoka/Kriemhild Gretchen splits into two components which then time traveled to the primordial Earth: Adam and Lilith of Neon Genesis Evangelion.
Hence Kriemhild's nature being similar to Instrumentality in many ways.

Witchification is the result of Sailor Moon putting Chaos "into the hearts of everyone."
In the Sailor Moon universe, there is a singularity out in space called "the Galaxy Cauldron" and was overseen by an entity called "Sailor Cosmos" (possibly a future future version of Sailor Moon) It produces all of existence, and in the manga; it's stated that the stronger the light is; the stronger Chaos is. Well, Sailor Moon stopped this cycle by sealing Chaos into People. This stopped the Galaxy Cauldron's production line. Magical Entropy began to set in. The Kyubey are actually agents of the Galaxy Cauldron who took over when Sailor Moon's actions negated Cosmos; the original Guardian of the Galaxy Cauldron. They found a magical way of releasing the Galaxy Cauldron energy...by releasing the Chaos trapped within the human soul. Madoka's sacrifice switched the cycle back.
 * All of this has happened before, and has happened again. The Enemy Within and the Enemy Without are constantly being kicked in and out of the human soul.

Madoka Magica sets the stage for the events of BlazBlue
When Madoka  actually contains half of the entire universe. The other half contains  Kyubey   got fired from his position for incompetence and was replaced by other Incubators, one of whom was Yuuki Terumi. Terumi trolls humanity incessantly because  and being around emotionless bastards like Kyubey drove him nuts. To compensate for the  the Incubators contract thousands of Magical Girls, which eventually reveals the secret of creating Soul Gems; unscrupulous human scientists then utilize the powers of Soul Gems to create Ars Magus and Sentient Weapons. The Nox Nyctores are all sentient, and affect the mind of the user in negative ways, because they contain the souls of Magical Girls
 * TA, TB and TC are also Incubators, and were planning to destroy Amaterasu  as part of a plot to disrupt the time loops and   Terumi   and disrupts the plot either because   or
 * Trinity and Luna were once true Magical Girls, but are now vying for time in Sena's body. Coincidentally, this means Platinum IS, in fact, a trap.
 * Bang's nail has the power to sever Boundary connections only because it contains a Puella Magi's soul.
 * Murakumo Units and dolls like Nirvana and Ignis operate on the same premise; they're Magical Girl souls with Restraining Bolts to force them to follow orders.
 * Arakune became a Demon/Witch/Whatever because he crossed over the Boundary. Phantom probably became a Witch the same way because
 * Tsubaki gets the power for her Astral Finish by invoking

Another theory is Madoka becomes  in an alternative continuity instead of

Kyubey is Mogget
No reason other than both being strikingly apathetic white supernatural cats of questionable allegiance.

Kyubey is a form of Nyarlathotep.
You have an amoral, eldritch jerkass critter who deals with teenage girls to in order to cause them to despair which ultimately results in human misery all around. His motivations for being a little cute critter to create magical girls are simple:
 * His form is what most people consider "cute" therefore lulling them into a false sense of security
 * He grants them wishes, which baits them into becoming Magical Girls
 * Their soul is put into a Gem for easier consumption and or manipulation when need be
 * Him eating Soul Gem's is actually him consuming what's left of
 * and thus amuses him.
 * His goal for creating  is actually a ploy...to awaken the Great Old Ones from their earthly tombs, with   as the catalyst.
 * If he is Nyarlathotep, then he knows  is a farce, as you know...he's Messenger to the LIVING CENTER of the UNIVERSE and all. He just crafts this reason as a a method to give a reason to what he does that won't destroy their mind, and most teenage girls aren't knowledgeable enough in that field to call him out on it.
 * He is  For his own amusement
 * Nyarlathotep has over 1,000 forms, the Mythos barely covers a 100 if that. It makes sense for him to have a form like this to make deals with mortals less difficult.
 * His entire plot of  actually is a method of   as   would generate a massive amount of power, which would be enough to awaken the living center of the universe, ENDING REALITY. That and we all know what happens next... on a immense scale of course.
 * Goddess Madoka then proceeds to destroy the Great Old Ones.
 * Or is it, cause perhaps that's what Nyarly wants you to think........

Nie R is one of Goddess Madoka's helpers.
Both Father Nier and Brother Nier. They're sometimes the same person, and sometimes not. (That sorta thing happens outside Space and Time.) When "both" Niers Ret-Gone'd him/themself to save Kaine; this got Goddess Madoka's attention.
 * And then that attention went to their universe, which was so incredibly screwed by The Corruption that it fell into her jurisdiction and she was able to guide everyone's souls to a better afterlife. (We actually see this afterlife in New Game+.)
 * Nier is a rare male helper in Magical Girl Valhalla; but he doesn't mind if it means his daughter/sister Yonah will have a peaceful place to go. Madoka's a good kid, anyways.

Soul gems are somehow related to Exspheres from Tales of Symphonia
Both soul gems and Exspheres hold the consciousness/souls of people. Both of them can turn their users in to monsters/witches if untreated. Both of them provide power boosts to their users.

Goddess Madoka is now in Gensokyo.
Anything that doesn't exist in the outside world exists in Gensokyo; thus by erasing herself; she appeared there. In between saving every magical girl turning witch in every timeline; and when she's not floating naked in the cosmos, her physical manifestation has a home. She tends to work closely with the Celestials and the Yami/Shinigami when working out a place for the magical girls to go.
 * Related to the above; the black cat that Madoka and the cast have hanging around them was in fact Chen, in her cat form. Having accidentally ran through one of Yukari-sama's gaps that transported her off-Gensokyo, she ended up in the show's OP, leading to Yukari's discovery of the Madoka 'verse and seeing the show. Her sympathy for Madoka and Homura (which reminded her of a certain maid that made damned good cake) caused her to weaken the border between hope and despair, allowing Madoka to break through it (when combined with the power that she gained from the time loops it became a certainty that she would succeed) during the finale. Madoka now resides with the rest of Gensokyo as a new early Stage Boss (though absurdly powerful and uses lots of arrow spam, like Sakuya's knives, Madoka is still new to the Danmaku genre so she's still not that 'powerful' when ranked in the Spell Card system. Plus she's not really trying to "win."
 * Highly related.

The entire show...
...resembles none other than Kamen Rider. Kamen Rider Ryuki, to be specific. See here for more details. For example:
 * Madoka is in the place of Ryuki, only she is still unable (or unwilling) to transform. Her reactions to Kyoko and Sayaka fighting seem to mirror Shinji's reactions when he first sees a Rider Vs. Rider fight.
 * Homura and Knight are both black and have Hidden Heart of Gold.
 * Also, her shield is similar to TaJaDoru's shield.
 * She also shares traits with Ryuga. Much like how Ryuga desires Ryuki to be one with him, Homura desires Madoka to be one with her... in the fan-interpreted way.
 * Mami and Scissors. Full stop. Yellow? Check.  Mami is not really evil, though..
 * She also shares some traits with Zolda. BFG? check. No Kill Like Overkill Finishing Move? check.
 * She also shares some traits with Raia in which she is one of the nicest Magical Girls besides Madoka much like Raia being one of the nicest riders besides Ryuki and is a Big Brother Mentor compared to Raia.
 * Kyouko is egoistic Magical Girl, and wields a stick. (With a blade at the end.) Yup, she's Puella Magi equivalent of Ouja.
 * She is also compared to Zolda. A Jerkass who often butt heads with Knight.
 * Sayaka fits Knight more. Her weapon is a sword, much like Knight's, she possess a cape and is colored blue, much like Knight's Super Mode, and
 * Kyousuke fits someone who would have become a Kamen Rider, Miyuki's friend, Yuichi Saito. Both were musicians whose careers are ruined by a broken hand..
 * As for Kyuube... Coming out of nowhere, asking for - all right, demanding - the contract that grants the transformation with one's wish? Is This Troper the only one to see the image of Kanzaki Shirou from this disturbingly Faustian Weasel Mascot?
 * Except that Kotohime path and tries to use the wish for himself
 * Also, wishes that come with a price? I think the Imajins would like to have a word.
 * Other Ryuki References include...
 * The witches' maze resembles Mirror World, in that it's where the battle between the protagonists and Monster of the Week takes place.
 * There is also the wish thing. Magical Girls make a wish and receive Magical Girl powers. Kamen Riders on the other hand get their wish after they murder twelve other riders.
 * When a monster is defeated in both shows, they drop an item that the Magi/Riders can feed to their Monster/Gem. Don't feed your Mirror Monster? It eats you.
 * Forming a contract guarantees a "no-exit" clause in either show.
 * There are also some resemblances with the American adaptation, Kamen Rider Dragon Knight. Kyubey is essentially a cute version of Xaviax: both take advantage of the magical girls'/Riders' moments of despair for their granting of wishes, and both play them like fiddles. Plus, Madoka and Kit both have Superpowered Evil Sides --
 * There is also an OOO resemblance.
 * There is also the ironic use of a catchphrase from a certain Kamen Rider. "Despair is your goal.".
 * Another possible translation to it is "Despair awaits you in the end.".
 * Ironically, the finale where
 * There are also a comparison to Kamen Rider Faiz.
 * And then there is a comparison with Sayaka and Kusaka. Sayaka's relationship with Kyousuke is Kusaka's relationship with Mari without the Yandere (we hope) aspects, uses a sword much like Kusaka,.
 * In Decade's tour of Hibiki's World,
 * Speaking of Decade,
 * Confirmed by Shinbou.
 * Source?'
 * Another possible translation to it is "Despair awaits you in the end.".
 * Ironically, the finale where
 * There are also a comparison to Kamen Rider Faiz.
 * And then there is a comparison with Sayaka and Kusaka. Sayaka's relationship with Kyousuke is Kusaka's relationship with Mari without the Yandere (we hope) aspects, uses a sword much like Kusaka,.
 * In Decade's tour of Hibiki's World,
 * Speaking of Decade,
 * Confirmed by Shinbou.
 * Source?'

Or, the show is basically a parallel world version of Armored Trooper VOTOMS.

 * Urobochi had openly stated that Chirico Cuvie, the lead character from Votoms, had inspired his life since his youth. Now consider Kyubey, one of the lead character from this show: shares similar name in Japanese, both are Determinator for their goals, . Alternatively, either Madoka or Homura can replace Chirico as resident Determinator since:
 * just like Chirico to the prolonged interstellar war.
 * Votoms' Opening Theme, Destiny of Fire (Honou no Sadame), describes Chirico's fate and feelings among the wars he faced. Now replace Chirico with Homura (which also means "fire" in Japanese), . And like Chirico fights for saving Fiona in the original,
 * is an obvious tribute to Votoms' original ending.
 * Need concrete evidence? This fanmade video from Niconico Douga. 12 of the Votoms' Next Episode Previews are totally synchronous to what happens in each Madoka Magica episode.

Kyuubey is an acquaintance of Chamo.
The Elf-Ermine was part of a small racket. His best friend was an absolute battery of Mana, and Chamo had been hired by certain members of the Magic World (an Alternate Universe to Mars) to "skim" from a mages's power through his Pactio's with other people. Just enough that nobody noticed. This energy was then purchased for "Chamo Dollars." The Magical World was in a crisis. It couldn't keep the power going to fuel it's own existence; and was hiring "scalpers" like Chamo to scrape together any Mana they can.
 * Kyuubey felt this was a good idea; but didn't go nearly far enough. Why scrape for power from a contract when you can get the lion's share? For a simple reality warp; contract with someone and then infect them with Magic Erebea. Suck as much power out you can; while having contractee's using fallen Magic Erebea users remains to stoke for a slightly slower burn. Then leave the area with the useable Mana as the surviving Magical Erebea's blow everything to hell.

Kyuubey is dealing with Slender Man, somehow.

 * Slenderman feeds off negative human emotions.
 * Witches are a product of such. (Also, Grief Seeds)
 * Magical girls eventually become Witches.
 * Kyuubey forces girls into becoming magical girls.
 * PROFIT!
 * Slenderman is the closest form the Incubator has to a real form.
 * Slenderman is the closest form the Incubator has to a real form.

Madoka is a Princess of Heart.
Kyubey is trying to get her to accept the darkness that comes with being a Magical Girl so he can steal her body and use it for his own purposes.
 * Alternatively, Kyuubey's a Nobody (he can't feel emotions, after all) and is trying to make the Puella Magi release enough hearts so that Kingdom Hearts will open for him.
 * So all we need is a Xehanort's Heartless Expy and we're set! "GRIEF IS THE SOUL'S TRUE ESSENCE!"

Kyubei is actually Hideyoshi.
Hideyoshi is fed up of being a fansevice bait and hence used some magical spell to turn himself into our dear magical pet.

Since he is a skilled actor, it explains why Madoka and co didn't suspect him.

Madoka Magica is set in the same universe as Inception.
One of the above WMGs pointed out that the magical girls are actually reality warpers, there is a chance that the Madoka universe is actually one of the dream stages and the girls are hooked onto the PAVIS machine.

I believe Chris Nolan somewhat has a hand in this series too.

Homura has to be a student/step-daughter of Nanoha from the future.
Just a guess seeing as Nanoha likes angsty Mahou Shojos. She totally digs them so much she started to collect them all over the universe. I'm guessing she was sent to stop a small white demon from destroying a world but failed due to a certain someone selling her soul to it.

Puella Magi Madoka Magica and Sailor Nothing take place in the same universe.
It just makes so much sense!

It's all another game between Bernkastel and Lambdadelta
Ahaha.wav.
 * Homura is a lot like Ange,
 * This. (*Madoka episode 9 spoilers.)
 * And this.
 * As of episode 10,
 * And that created witch is .....
 * Unfortunately for Bern, her new Unless she actually doesn't mind AT ALL.
 * Kyuubee (Beatrice) is trying to get Madoka (Battler) to become a magical girl (believe in witches) and puts her in increasingly desperate situations to make her make that decision as everybody she knows and cares about is being killed left and right (increasingly inexplicable murders where everybody is dying).

Kyuubei is actually a representative of the World...
He grants miracles and in return the contractors became Magical Girls (fancy name for Counter Guardian) who will fight whenever a factor in the extinction of mankind (Witches) is detected.
 * Strongly jossed in episode 8.
 * Alternatively, if Alaya is the counterforce of humanity and Gaia is the counterforce of the Earth, Kyubey is the counterforce of the Universe as a whole.

Madoka is Archer

 * Or....

Madoka's soul is already outside

 * She doesn't need a container and if she turns into an MS she can fight using her soul as a weapon. A combo of Eirin and Youmu.

The Witches are True Fae, and Magical Girls are the retribution of the angered universe of Changeling: The Dreaming.
When Dreaming was discontinued and then replaced by the New World of Darkness line, Changeling: The Lost, it rebelled against the drastically different ideas of what the True Fae are, but the displaced Changeling spirits had no recourse of their own. Thus they created Kyubey, according to the new laws set out by Lost. The real nature of the Contract is that it's actually a Pledge: in exchange for becoming a Magical Girl, they agree to fight the True Fae and are likewise entitled to a wish, and weapons with which to fight them, for life. This is an extremely powerful Pledge, and since Kyubey, despite being made to adhere to the rules of Changeling: The Lost, is still fundamentally tied to the concepts of limitless fancy and absolute belief, making it possible for the Fae powers manifested in the Magical Girls to cut through the Hedge and kill True Fae in their own realms. However, if a Magical Girl's soul gem becomes corrupted, and the result is a Changeling, not another Witch.
 * With the revelation that, it seems more likely that magical girls are just Changelings, while Witches are True Fae, since
 * The similarities go far, far beyond that. Witches are worlds unto themselves, beautiful and terrible worlds with surreal landscapes and shaky physical laws that mirror the witch's former personality's dreams in a very twisted way. Yet, witches are also lifelike characters, strange as they may be, who exist within the world which they are, and are also a host of small faceless minions in same. Girls who are exposed to witches often return to this world feeling like aliens, like everybody else is strange and distant and the world itself has changed forever. By contract, some of them gain powers similar to the witch's own they use to fight them, not knowing that as their powers grow and they become more detached from humanity, they are just getting closer to becoming witches themselves... There is just no end to this!

This is Shaft's version of Claymore.
Kyubey decided to create magical girls that would remove despair from human lives, but ended up creating witches.

Voldemort was formerly a Magical Guy.

 * AND NOW HE'S A WIZARD. His witch's kiss is The Dark Mark.
 * He managed to keep his original Soul Gem (Horcrux) because he tricked Kyubey and blocked his power, so not all his soul was poured into the gem. He didn't want to relinquish control of the situation. He slew Witches and members of the Wizarding Community to seem like a normal Magical Guy (R.I.P Myrtle...) but learned how to make his own Soul Gems/Horcruxes and, wanting absolute immortality and invulnerability, did, evading Kyubey and killing more people, increasing his power. Unfortunately he 'matured' into a full-blown Witch after graduating from Hogwarts and became the Big Bad we all know today. He was able to retain human form and speech because of his alternate Soul Gems/Horcruxes.

Madoka Magica is actually a story written by Drosselmeyer (contains major Princess Tutu spoilers, but none for Madoka)
Drosselmeyer was a author who could He loved writing stories depicting eternal tragedy and despair. After he found a way to write such stories in the afterlife and decided to write Madoka Magica to make up for the "failure" of a story that was Princess Tutu. So far, he is very much succeeding where he failed the last time.

Kyubey is the Millennium Earl.
They operate in a similar manner, "helping" people who aren't in much of a state to refuse. And they both have almost permanently frozen-on smiles.
 * You might be on to something. Kyubey also collects the energy created when Akuma are formed and when they evolve. Maybe the Noah are Magical People who managed to stay 'in between' Magic Girls and witches? Innocence are really Soul Gems too! Maybe Akuma and the Noah are all witches, too? But the Noah might be "evil" Magical People? Maybe Road designs all the Witch's Barriers, or they're all her different Dream Worlds?

Kyubey is O2.
Kyubey's second set of ears resemble O2's wings, and he even has halos on them.

02 is a witch.
It has the same imagery as a witch's barrier, and its power lies in strong negative emotions, including grief. Dark Matter possesion could be a parallel to a witch's kiss, except it just makes people evil instead of suicidal. It being killed in Kirby's Dreamland 3 and reborn means that Kirby didn't destroy its Grief Seed.

This takes place in the same universe of Bokurano.
More specifically, in one of the universes that was saved. However, despite being saved, the universe began dying, and thus a new "game" had to be created to save it.
 * Could this mean that Dung Beetle and Kyuubei might be related to each other? Or the same person?

Kyubei is Kyubi
One of Kyubei's names is QB. Saying QB gets you Kyu and Bi. But them together and you get...

Kyubey and the other Incubators were created by the Eldar
Think about it. Entropy is also called Chaos by some people. The Eldar have a 'Fuck off all other races in order to save ourselves' mentality, and Kyubey loves giving out half truths and Jedi Truths. Saving the universe my ass! They just want to prevent the heat death of the universe because maximum entropy would allow the Chaos Gods to enter and eat them alive.
 * Kyubey's "sacrifice tortured girls so that Entropy is appeased and doesn't eat them alive" agenda is basically the same with the Dark Eldar's relationships with Slaanesh.
 * Speaking of Eldar, isn't their plot to create Ynnead basically their own version of Kriemhild Gretchen?

The Birth of Chaos is
When the Witches existed; they exist as  in their own personal Hell (their Barriers) where Entropy (also known as Distortion or Chaos) and Negative Emotions can be condensed as fuel for physics-defying Psychic Powers, essentially acting as smaller and more controllable versions of The Warp. However, knowing that Madoka's wish, all the homeless shards of Entropy have no choice but to gain sapience themselves and pave a new source of Despair, called Daemons. Sure the daemons are less forgivable (and in fact, less powerful: if Episode 12 is to be believed.) than Witches, since witches , while daemons are made from wandering Chaos, but fast-forward to the events of pre-40k (expansion of the human population to trillions, the Horus Heresy, Birth of Slaanesh, and the Eye of Terror as a whole) and you can see what the daemons have become, i.e., the Ruinous Powers of Chaos, with their own Hell/Witch Barrier (The Warp, or Hyperspace Is a Scary Place).

Not only that, It's safe to say that Magical Girls and other people who have encountered an Incubator may have been under Excommunicate Traitoris under the Ecclesiarchy or Inquisition due to using the daemons as a Source of power (Or they're just burned along with the majority of psykers from sheer superstition if they aren't fed to the Emperor). Guessing that you've seen the horrors of 40k before, You can easily say that  is a lot nicer than an exterminatus. And even an Exterminatus is one of the "nicest" things a planet can go.
 * Alternatively: Madoka grows a spine and manifests the Emperor of Mankind in an attempt to fix her mistakes. Well they're both Jesus.....
 * Actually, the Emperor of Mankind existed before Madoka; though its entirely possible that Madoka is responsible for giving the Emperor his Omniscience...Oh wait.
 * But since the Emperor was born in REALLY old times (8000 B.C.), She may have ONCE created him as an agent of hope, continuously serving the years masquerading as notable figures. And became the last line of offense for humanity when it went downhill. Considering that she's a Goddess who apparently redid everything else...she had a lot of time offscreen.
 * I usually think of Madokami as the primary consciousness behind the Astronomican.

Kyubey is from Logopolis
Kyubey's goal is to decrease entropy in the universe and prevent it's destruction, the same task that the Logopolitans had given themselves to. The 'Puella Magi' system is a replacement for the 'Block Transfer Computation' and CVE methods that were in use before the Master interfered.
 * The Puella Magi system is the backup system the Master threatened to destroy.
 * Alternatively, thanks to Madoka's intervention an improved version of the Block Transfer Computation replaces the Puella Magi system (although it's more literal since demon-harvesting does involve Kyubey eating literal blocks).

Mami is Mima
Magical girls are cursed to become witches. Due to the nature of her wish, Mami managed to become one even after her "death". However, in the process or just over time she lost most of her memories, even the order of the kanji in her name. While she is by all appearances a ghost, Mima insists that she never died, and is "just a soul". Hmm...
 * YOU DARE INVOKE MIMA ON THIS PAGE? Oh yeah, you asked for it. TOUHOU EPILEPTIC TREE TIME!
 * Madoka's sheer potential is because she's part youkai/devil/demon/spirit/god/whatever, with a typical hax Touhou ability.
 * Kyuubey was made by Yumemi Okazaki.
 * Yukari Yakumo is an insanely powerful Witch- the gaps are actually her barrier. Fortunately, she seems to be much nicer than a standard witch, probably because she didn't need  to become one.
 * Sayaka is Cirno. Don't ask how.
 * Youkai Jesus will/Shinki will save the day.

Creators of the Incubators will soon be destroyed
And it will be the Anti-Spirals who will do the deed. Because, Creators of the Incubators are doing exactly what Hanrasen are fearing - they are introducing more and more energy in the universe. Sure, without the emotions to do it directly, they are taking a longer way than most, but it's still there!
 * The Anti-Spirals doing something GOOD?! ... I actually like that.
 * Alternatively, the Incubators realized that Madokami's new system works so well it overloads the universe with energy. Cue them becoming the Anti-Spirals.

Mahou Shoujo Madoka Magica is an alternate JoJo's Bizarre Adventure timeline
Kyubey has Dirty Deeds Done Dirt Cheap. Homura has Za Warudo or Made In Heaven. Mami has Sex Pistols. Madoka might get Gold Experience Requiem.

Kyubey's race created Zonder Metal
Zonder Metal was designed by an alien race to turn the stress of humanoids into energy, simultaneously solving There Are No Therapists and providing an unlimited source of power. Then it became sentient and starting merging with people to amplify their stress and turn them into monsters. Zonders are fought by guys using crystals powered by courage (operating on similar principles to Zonder Metal itself), and are defeated by removing their cores and turning them back into humans. Hmm...

Akemi Homura is Izayoi Sakuya
Don't think too hard on it. You'll just get a headache.
 * Za Wurdo with bullets and rockets? And an ice cream truck instead of a steamroller!
 * In one of the timelines where Homura fails to save Madoka, Madoka eventually transforms into a most powerful witch capable of destroying the world in 10 days. That witch is Flandre Scarlet. However, due to a wish Madoka made, her human body was turned into a vampire, who took the identity of Remilia Scarlet and was able to keep Flandre from doing any harm by assuming the role of Flandre's "sister". "Madoka" then found the Homura that was still in that timeline, gave her the name of Sakuya Izayoi, built a mansion for the three of them, locked the witch in the basement, and eventually moved the three of them along with the mansion to Gensokyo to keep the world safe. (And now I have a headache.)
 * Hold on a moment. Madoka becoming Flandre makes sense, but the 'older sister' Remilia is instead Sayaka, now a rather arrogant and cynical self having been brought back from being a Witch. So to 'protect' Madoka, she seals her in the mansion. Meiling's shoes are filled by Kyoko, who now sleeps a lot because she never had time to rest as a Magical Girl (just like near-starvation caused her to take on Big Eater traits). Homura is Sakuya, again as always, but as well as that her 'first' self - the Meganekko Shrinking Violet - has become seperate from her 'Magical Girl' za warudo time-stopping self and now acts as a 'guest' of sorts, pretty much living in the library to try and find some way of bringing unstable vampire Madoka back to her human self.

Kyuubey is the Anti-Spiral King
He's an alien with the power to change reality. His goals are to preserve the universe, and he's tapping into an illogical energy source that breaks the laws of physics. His purpose in life is basically to save the universe by imposing absolute despair upon humans. The only difference is that he's trying to farm and control Spiral Energy rather than destroy it.
 * This Troper thought the race that sent Kyuubey was more akin to the Spiral races, what with the continued addition of mass/energy to an otherwise closed system, which may still lead to disaster. *coughSpiralNemesiscough*
 * But you need emotions to harvest Spiral power, while the Incubators themselves are emotionless (making them incapable of using magic).

The Witches' Labyrinths are Reality Marbles
Why is that? There are probably more similarities that I can't think of right now.
 * Both are the representation of the heart of the caster. Just like Unlimited Blade Works is a representation of Archer and his struggles,  represents her desire for attention and wish to be loved by the person she cared about the most, which is shown by the concert.
 * Witches can only live within the labyrinths, and that is the same as Nero Chaos who can only live by sustaining the reality marble that composes his body.
 * Inside the Reality Marble, the caster has the most power available to him/her.

On a similar note, Soul Gems are the Third True Magic
That is, "Materialization of the Soul".

Rebecca Black made a contract with Kyubey.
Her wish? To become popular. Looks like she's already achieving it. Of course, Kyubey being Kyubey, it's not exactly the popularity she wished for.

The show is actually a retelling of Legacy of Kain. Homura is Kain, Madoka is Raziel, and Kyubey is the Elder God.
Like Kain, Homura is stuck in the position of choosing to let the world be destroyed or lose something very precious to her, so she in order to Screw Destiny. Kyubey of course wants to keep the status quo, since he needs Puella Magis 'souls. Madoka is the only individual capable of changing fate, so Homura and Kyubey are both battling to try and maneuver her to do what they want.

Kyubee is a Japanese Brush God.
Compare how the Brush Gods of Okami (especially Chibiterasu from Okamiden)) look and [[media:kyubey001 9212.jpg|QB]].
 * Or the Brush Gods plus Ammy dear are Incubators. Just the emotional/benevolent/mentally unstable kind. In line with the TSAB theory down below, when in doubt blame Belka. Maybe they're some form of modified familiar and the reason they're not active in the present is because they've been cut off from whatever energy source the blasted weasels have. They did have spaceships in that game after all... and now I have plotbunny.

Kyube's mentioned advanced alien civilization is... the TSAB.
The TSAB is an advanced, multi-dimensional civilization that uses magic as an environmentally safe energy source. Unfortunately, they don't realize they're using the potential energy of the universe directly, in massive amounts. Kyube knows though, and though he can't stop the TSAB, he can at least make sure their squandering use of energy is contained, by creating more magic/potential energy.

And now you know why there are so few mages on earth.

Yes. I've just completely destroyed Nanoha's noble intentions for about one episode. /人◕ ‿‿ ◕人\

The Kyubee are Lost Logia.
The Jewel Seeds, massively powerful Lost Technology that collapsed dimensional walls and turned people into monsters because the safety settings were lost. Sounds familiar?

Human mages have always been rare; no matter what era or dimension. In one of the old worlds; the war with their neighbors was all but lost. All of their active mages were dead; and while some of their familiars were left; they were about to die/lose sentience without their masters. A few people who were given command altered the familiars. They no longer required masters to exist; they could create multiple bodies, and their job was to create mages and energy to "save their universe." (The reprogrammers were dramatic and patriotic) The war had cost most of the adults; and women were more prone to magic than men so they focused on them for logistical purposes. These Familiars would Incubate the next generation of Mages. It was decided that the best way to ensure loyalty would be to program them to be emotionless and be only dedicated to their goal. The augmented familiars went through the population; and by "forcing" non-mages to cast a Reality Warp even though they don't have Linker Cores (making a Wish); they burned part of their permanent Life Energy into positive and negative energy to create a type of pseudo-Linker Core/Device fusion Cast From HP and the owner's emotional state. Soul Gems. Unlike normal Devices; these did not use computations to protect the owner from being directly linked to Magic.

Magic Users were regained; at terrible cost. Untried in combat; many of the new batch of mages quickly fell. But those who survived fell into despair; and their Soul Gems collapsed. Their despair; running unchecked through the magical channels blasted open by the Reality Warp; turned them into terrible monsters; and the dimensional walls surrounding the old world collapsed.

The familiars, now the Incubators, viewed this as a complete success. The remaining witches were "safe" from the old world's enemies. They left the dimension; to fulfill their programming. To save the universe by creating magical energy.

Worlds visited by the Kyubey often experience massive jumps in technological and magical advancement due to the Reality Warp; sometimes without the social infrastructure to handle this. Often their populations fall to rampant interwarring sessions or are slaughtered by witches and the world becomes a danger to the dimensions surrounding it, requiring the world to be destroyed or dimensionally quarantined.

The TSAB considers the Kyubey to be Alpha-level threats and they are to be destroyed upon discovery via Arc N Ciel.


 * In any universe affected by Madoka's wish; most of this story is still true. Any time the old world lost a battle with its new mages; the opponent could never hold that area for long due to Demons that sprang up due to weakening world walls to the Spirit World (where Summons come from). The Puella Magi could not keep up a war against their countries enemies and their own Demons; and they died. One of the last Puella Magi of that world made a wish to send all their non-mage population offworld. The Incubators still escaped through their own means. Planetary destruction of worlds visited by them is still possible due to Demons, but far less likely.
 * The TSAB is divided on Incubators. While there are some who argue that the wishes possible are worth it; others feel the risk is too great. They have enough problems with Lost Logia; why add Demons? Sometimes they don't have a choice; and feel that having anyone who can fight Demons and Lost Logia is better than having noone who can fight Logia alone.


 * Most TSAB believe that the process doesn't create demons, but rather opens gateways to a Layered World where emotional states have physical form. Usually the TSAB prefer to strengthen the dimensional barrier; there is debate on whether relying on beating physical manifestations of negative emotions is healthy; as it bypasses people and society from naturally addressing their own issues.


 * Most Administrated Worlds ban Incubators; and the few that allow them (usually due to critical low mage population) have it very regulated. Incubators are not allowed to contract anyone without permission from the TSAB; and contractees are briefed by experts on how to make and word their wishes (even better if the TSAB can "buy" a wish by using their resources to accomplish the goal instead. The wish can then be used for less emotional goals; thus giving a better chance of a favorable result). "Puella Magi" Mages have regular psychological check-ups; and many are assigned professional teams ("Hope-Givers") to keep their spirits up. Every last one are, of course, employed by the TSAB. Attempts have been made, with no success, to restore Soul Gems to a Puella Magi's soul; or to modify Soul Gems with Devices and/or traditional familiars.

The Incubators are unchecked on Non-Administrated Worlds.

Kyubey was created by the same race as Kyrios
Kyubey: An artificial race that exists to harvest magical power from girls in order to prevent energy death.

Kyrios: A machine that uses the power of a magical girl to control the flow of energy across the multiverse and prevent the energy death of any one world.

Kyrios even has an "artificial" magical girl guardian who acts as its protector.

The series takes place in Instrumentality.
QB is a rogue spirit breaking the peace. Come on, it's obvious Madoka's world is a warped up version of Evangelion's.
 * Morning Rescue is LCL!

The black cat in the OP is
With no explanation for that cat, and the revelation of, there's no doubt. Fate Averted! ...Or not.
 * Homura's soul gem is really a Temsik fragment, and on top of her time traveling, her Hyperspace Arsenal is a actually a variation of Missile's ability to swap the places of objects!

Kyuubey is the bastard son of Tzeench and Slaanesh.
For he is an Eldritch Abomination who weaves Machiavellian schemes and takes perverse sustenance from suffering and warped innocence.

Puella Magi Madoka Magica is based off of Drawn to Life!
WARNING: THIS IS A WALL OF TEXT. ALSO I REPOSTED IT BECAUSE IT SUDDENLY DISAPPEARED INTO NOTHINGNESS.

Lets take Mami for an example. She's based off of the Mayor. The Mayor has an old-fashon clothing style. So does Mami. The Mayor is an old person. Mami is the oldest looking of the group. Also, one of the magical girls (I think it's Mami) made a wish when she was. This could represnt. Houmra. This could represenent. Madoka is the Scrappy and also the Woobie, kind of like how. Wilfre and Kyubey are both (at least acrounding to this wiki) are. Madoka's  represents. And the older Madoka transforming Madoka in the opening? That represents ! Madoka opening her eyes in said opening? Her crying tears of joy holding the cat? Madoka holding Kyubey in the final shot? Heck, maybe it IS part of the Drawn to Life series! This is the Drawn to Life 3 we been all looking for! Wilfre must have put Jowee in a nightmare, and all the paraells to Drawn to Life in the show are all his memories leaking through! The Series might end when he finally wakes up, and still thinks he's Madoka. At first we see it from his point of view, as Madoka runs trying to find her friends, paraelling the seane in the opening where she is running. We see her running for days until she finally gets to his Village, where we finally see Jowee crying out for Madoka's friends. Thats when we reallize that Madoka and her friends were all part of Jowee's mind, messed up by Wilfre. The ending credits may paraell these events, Madoka walking past her friends represents her train of thoughts just before making the wish that would wake up Jowee, and Madoka running repressents "Madoka" running to find her friends, her floating in the mask repressents "Madoka" trying to blend in with the Raposa, hoping they might think of her as a visitor and not knowing that "she's" on of them. As if the series wasn't whammy enough...

Charlotte and Charlotte Dunois are
It is stated in her bio that Madoka Charlotte loves cheese. Charlotte Dunois, for her part, is French and therefore a Cheese-Eating Surrender Monkeys...

The Incubators are from Magical Land.
That kind of cutesy sadism could only come from Esmerelda and Punie. Paya even called her a "true witch".

Kyubey is an apprentice of Zordon.
He has sought for "five overbearing and overemotional humans" who happen to be red, blue, black, yellow and pink. Unlike Zordon, A. the "overemotional" part is utterly crucial to his plans and B. he's not as successful as the floating head was.
 * Also, had Kyubey gotten his way, Hitomi would become the Green Ranger, just because both are green.

Homura's story is based in a Vocaloid song.
More specifically Repeat. And if one analyze the lyrics, it means she'll become a witch in the end.

Homura's story is based off the song W
Here are the lyrics.

Walpurgis Night is Chernabog
Night On Bald Mountain takes place around Walpurgis Night, where a powerful demon arises, much like in Madoka.

Madotsuki used to be a Puella Magi
But she learned the Awful Truth, and also had to watch her fellow Puella Magi die or turn into Witches. So she gave up and turned into a Hikikomori, thinking that she would at least enjoy some normal days before turning into a Witch. However, things weren't so simple. The memories of her time as a Puella Magi still tormented her in her dreams. For example, the different areas are Witches' lairs, the Toringen are familiars, Poniko was one of her friends, and. And so, after having all these fucked-up dreams for so long, she finally decided to commit suicide.

IT ALL MAKES TOO MUCH SENSE. Here, have some explanations with visuals:


 * Another version of Madotsuki's outfit; Madotsuki first meeting Kyube,Madotsuki and her fellow Magical Girls; Poniko going Witch, alternate rendition of Madotsuki facing Uboa - notice Poniko's empty body being held within it; the first time Madostuki got sucked into a Witch-Realm after witnessing a Witchkissed friend stab themselves; Madotsuki finally turning into a witch; and Madotsuki's witch form (Danbooru links, may contain NSFW ads).
 * The fate of her friends? Monoko died a horrible death being mutilated by a Witch (hence her odd misshapen appearance when you use the Stoplight on her), Monoe couldn't take it and faded away after smashing her Soul Gem before she could suffer Terminal Corruption, and Poniko became the Witch Uboa (Which particularly traumatised Madotsuki since it happened during a sleepover) - I like the implication that she was having a sleepover with Poniko to try and keep her friend's spirits up, but Poniko's trauma was too great and she became Uboa right in front of poor Madotsuki in spite of an attempt to mercy-kill her by stabbing.
 * While everyone assumes that Monoko's deformities are indicating that she died, in this case she may have become a Witch as well, and her growing multiple arms represents her transformation. Stoplight!Monoko may even be the witch Patricia, though that's a bit of a stretch. Also being killed and witching aren't mutually exclusive, unless the Soul Gem breaks. Monoko could have also been horrendously injured and then witched as a result of it; witching out by running out of magic while regenerating from horrific mutilation is a pretty grim fate.
 * Alternatively, Poniko's Witch form is the bleeding multi-armed monster in the background of the area Uboa takes you to. Uboa is its familiar. Witches tend to be more complex-looking then their familiars, after all.
 * In Madoka Magica, one of the Witches Fought was H.N. Elly, the Hikkikomori/Box Witch. One of her primary Motifs was Flying Wings and some Checkered patterns. Guess the Yume Nikki character who is a Hikkikomori and has checkered patterns and flying as motifs normally associated with her. And don't the bluish things in this picture of Elly's barrier look an awful lot like Mars-san?
 * There's lots of symbolism behind Madotsuki's powers in-dream, such as that decapitation one being the time she lost her own head but somehow survived because her Soul Gem was intact. The Crashing event in the Famicom World could have been an combination of the times her old RPG cartridges glitched and the time she got stuck inside a Witch's maze after getting separated from her friends, only escaping once they beat the Witch. The Toringen? They were beefed-up Familiars that managed to survive her knife attacks, and their attempts to kill/imprison her traumatized her badly.
 * Alternatively, all the the powers/eggs that Madotsuki collects within her dreams could represent all of the Soul Gems of fallen Magical Girls that Mado wishes to save. Soul Gems are egg-shaped by default, are they not?
 * Mars-San is a Witch and Masada is its familiar. The Spaceship and Mars areas are Mars' realm. Masada's duty as Mars' familiar is to take Magical Girls and other victims deeper into Mars's realm. Also there are multiple Masada-familiars that pilot the "spaceship"; this is apparent from Masada always appearing to respawn in front of the piano whenever you exit and reenter the room after killing him within the game. Furthermore, befitting the creepy Puella Magi series, the Masada familiars look neither Bishounen nor Moe as commonly depicted by the Yume Nikki fanart community; they acyually look nightmarish like this. And concerning Mars-San, the Magical Girl who became Mars was really interested in astronomy and science fiction, explaining Mars' space travel-themed Witch realm. And once Madotsuki encountered and started attacking Mars, she gained the realization that Witches were more than simple Eldritch Abominations. Even as Madotsuki attacked it, Mars wouldn't fight back and continued to weep quietly to itself...
 * So when Madotsuki finally acquired all the powers, she realised her own Gem was fading and tried to off herself before she became a Witch. Unfortunately, given the Familiars that surround her broken body in the ending, she may have become a Grief Seed before landing. ~the User:Ace Of Scarabs

Mitakihara is a small-scale offshoot project of the Matrix.
Some speculation concerning the series has brought up the question of why Kju͍u͍̥bee (in IPA spelling) actively searches for ideal prepubescent girls to enjoin in his contracts; given that his race, being capable of great scientific feats, could certainly have grown and conditioned such creatures from infancy to feel strong emotions in response to especial stimuli. Further rumination on the dilemma led to the conclusion that they were, in fact, doing so; and they were, in fact, not alien, nor a race at all.

This would explain why the inhabitants of strange Mitakihara have access to the very finest of technology, and why it seems to contain such a mix-up of famous architecture, while there is no reference at all to any wider world: it is a virtual Paradise carefully constructed from models of the Earth as it might be in AD 2010. The entire world was created by the machines as an experiment to see if a slightly different management model would be successful in generating more energy and encountering fewer human problems than the mainstream Matrix.

To prevent the inhabitants from paying attention to the world around them and possibly realising that it is a simulation, the human batteries are convinced that they are not only living ordinary, humdrum lives, but are being drawn into a sudden, inexplicable and progressively more terrifying phantastic scenario in which their ultimate doom is to go mad with grief, and become a witch. (It is plausible that humans wallowing in the depths of despair produce increased amounts of whatever nebulous energy the machines derive from them, as well.)

The Incubators are therefore the quintessential Agents, whose purpose is to facilitate and perpetuate the cycle of grief and madness; they can appeal to governing powers to conduct alterations, such as gaining new bodies (provided they keep the internal balance of mass by 'eating' the old body), eliminating injuries, and resetting the universal clock, "reloading the Matrix" (though the reformatting of human minds is somewhat incomplete, and may leave traces).

The most prominent evidence in the favour of this is the presence of a character from the Matrix in the anime. The much-speculated-upon black cat of the Opening first appeared in the original Matrix movie: notably, just before time turned back, and Agents arrived.
 * Therefore, Madoka is The One, meant to "reload the Matrix".
 * I imagine a situation where the Kyubey before Madoka's cosmic reeboot returns to the New World, now filled with Despair and having become the Madokaverse's equivalent of Agent Smith.....

Lain Iwakura is a magical girl.
Her wish was apparently related to computers. She uses it to save people from suicide, by at the same time her surrounding becomes more and more screwed up. At the end of the series she becomes a witch and deprecates herself from reality.
 * Alternatively, Lain ended up doing the same thing as Madoka, and Madoka is the reincarnation of her, which made Madoka do the same thing as Lain did.

The witches are really Shadows.
They've got all the major trademarks: born of the protagonist's deepest regret/insecurity, having powers similar to theirs and some kind of thematic appearance (I.E. Shadow Yukiko is a bird in a cage because Yukiko felt trapped,  was a mermaid because of Sayaka's unrequited love.)

== Related to the above, Walpurgis Night is actually the witch form of. == Looking at her card, you can see a couple of parallels.

Irisu is a Puella Magi.
She wished for her rabbit to come back, and well...

Ai also became a Puella Magi.
Only in the normal and good endings, though. Yuuki's only showed himself to her so he could warn her about Kyuubey. After all, your targets becoming witches isn't exactly good for your quota, now is it? In the bad ending, he succeeds in preventing her Puella Magi-fication by taking her soul, and the good ending has her in.

What about the normal ending? Charlotte had to come from somewhere, don't you think? Just replace "cheese" with "rice cake" and they're practically identical.

Madoka is the 332nd.
Remember what happens in episode 12?
 * ...and
 * ...and
 * ...and

We know who the last is. We also get to meet him. He's

You can't say it doesn't make sense.

Madoka
...specifically, an Umineko witch. Yes, an army of Umineko witches, that are now capable of preying upon the multiverse. Just as Bernkastel planned.
 * There's also the fact that  sounds like a Logic Error.

Madoka became The Nexus
Just look at it.

Counter Guardians are Puella Magi
Because Joan of Arc has been listed as both a Puella Magi and a Counter Guardian. Both involve making contracts with an emotionless entity for power, at the cost of fighting endlessly. The only depicted Counter Guardian is in a similar mental state to Homura and even has similar powers. The differences can be explained as the result of Madoka's wish.

Homura's witch form is Bayonetta.
Because that would be awesome.

The Witches are Heartless
Think about it. A Heartless is formed when a person's Heart is consumed by darkness, transforming them into a Heartless. A Witch is formed when a Mahou Shoujo's soul gem is wholly corrupted/consumed by darkness, transforming them into a Witch. "Heart" and "Soul" can both be translated as kokoro, a Mahou Shoujo separated from their soul gem is very similar in behavior and appearance to a person separated from their Heart, and both Heartless and Witches can only be truly harmed/destroyed by certain types of magic.

Medusa and Arachne were Puella Magi.
Simply based off the curiosity caused when it came out that. What if two of anime's most cruel witches were once Puella Magi? Medusa's color scheme would be green and her weapon a bow and arrow (her snakes resemble arrows) while Arachne's color would be purple and her weapon a net that resembles a spiderweb. Their lairs aren't hidden because this is Soul-Eater-land...Baba Yaga castle is still pretty surreal, just not hidden behind a dimensional wall.
 * Or lairs in the PMMM world are beyond portals to the world of Soul Eater...

Every Magical Girl will !
I mean every Magical Girl ever. If the reasoning is that  every female out there with a transformation sequence is doomed. Usagi? They're still trying to figure out how to give her grief. (And her Soul Gem is in the tiara.) Ahiru? We will one day see a witch with duck wings and a ballet-themed lair. (Her contract was with Drosselmeyer, not Kyubey.) The girls of the Western takeoff WITCH? Look at the title, my friends.
 * You missed an episode, . Also, the Sailor Senshi's Soul Gems are obviously their Sailor Crystals. Also, they're not witches it's just their initials.

The series is a session of an even earlier version of Sburb gone off the rails.
...What? Don't look at me like that.
 * Supporting this, the bits and pieces we see of the afterlife are similar to the concept of dreambubbles, which the dead reside in once they no longer have a body to go back to. Plus Madoka basically has the same role that Aradia ends up having: Guiding the dead so they can move on and live their afterlives in peace...even though their environment is basically a wall between them and countless eldritch abominations.
 * Recent events of Homestuck aren't helping, what with

Alice Liddell was a Puella Magi.
She wished for the story Lewis Carroll told her to come true. "Wonderland" became her barrier.

The Incubators are a creation of the Jjaro...
...And one day, Durandal found them and activated them in order to buy more time to figure out how to escape the inevitable closure of the universe.

Yuuko's magic is related to the Incubators
Either they share the same source(Everything has to be balanced in the end) or either of them outright stealed the technique from one another.
 * The Wish doesn't seem to be something Kyubey himself has power over; rather it's some kind of ingrained feature in the human soul. And "Equal Part Despair and Hope" that they generate do sound like Equivalent Exchange.

I.M. Meen takes place in the Madoka Magica universe.
I.M. Meen is a Warlock who made a contract with an Incubator who goes after boys instead of girls. His Grief Seed is worked into his book so that it functions as a portal into his Barrier, the Magic Labyrinth of I.M Meen (Barriers are even sometimes referred to as Labyrinths). His "pets" are his familiars, and the "special kind of guy" he mentions as his magic being from in the theme song isn't himself, it's his Incubator. Speaking of his theme song, he says "I've got a little secret that'll really make 'em cry!", which refers to him capturing children so he can harvest their despair. His face looking different in each scene isn't the animation being Off-Model - what makes his Warlock form so surreal is that his face keeps morphing on its own, despite the rest of his body being able to pass for a human. Also, notice how in the intro, the kids are live-action in the very first shot where Meen points at them, but after that they're cartoons - the graphic style of Meen's barrier is crude CD-i style animation, and the kids changed to his style when they were sucked inside. This also explains why he hates children studying even though he knows magic - he didn't learn magic on his own; he obtained it through a contract. As a Magical Boy, he might have been a nerd who spent his time reading fantasy novels when he should have been studying, which is why his minions are ordinary trolls instead of Daliesque monstrosities. His reluctance to live in the real world caused him to flunk school and drop out, the despair of which caused his Soul Gem to go dark. As a Warlock, he took his revenge by tricking studious children and sucking them into his Labyrinth to get back at his classmates that succeeded where he failed. This is also why he's so bad at grammar - his dropping out of school was exaggerated to the point where, as a Warlock, he can barely spell. His teleportation ability reflects how he wanted to get away from his peers and be left alone. Bet you won't look at I.M. Meen YouTube Poops the same way again, huh?

Another rare Magical Boy was the boy who would become the Unlosing Ranger.
His wish was to save his sister from the Monster of the Day that had kidnapped them both. Being male, he got the wish; (making him strong enough to survive the beating the monster gave him) however it didn't generate the same kind of Mana that girls got for some reason. (Hence the Incubators rarely bothering; he was just an experiment.) The Equivalent Exchange was the eight years of hell his family gave him after this. He never turned Witch or faded because he has an abnormally high despair threshold. However, once he acquired the Chakra Belt; his ability to withstand Despair caused him to be able to generate a equal counterforce of Hope.
 * Post-Madoka change; the Unlosing Ranger eventually disappears into the Bizzaro Universe; to battle manifestations of despair until he dies., but L'Etranger will likely have a say in that.

"Slender Man" is a witch.
It explains virtually everything about Slendy: static has been used at least once in the anime in relation to witches; the world warps when Slendy is near because the viewer is caught within its labyrinth; many of the strange things that happen can be caused by a Witch's mark. It probably made a wish related to protecting children.

Madoka Magica exists in the same universe as Shugo Chara
Think about it. Wishes/hopes that make a person transform into a Magical Girl. Sounds familiar? Shugo Chara is set several centuries before Madoka Magica. The Guardian Charas are actually a prototype of the system Kyubey uses for Puella Magi. Back then, a person could make multiple wishes and could have multiple forms. The Eggs back then are equal to the Soul Gems of now. After experimenting with multiple people, Kyubey realizes that girls are much more emotional then boys, so he develops the system to only use girls. X-Eggs are equivalent to a corrupted Soul Gem, but when Kyubey realized that if X-Eggs are crushed, all the energy goes to waste. So then he developed Witches and thus the energy making machine was born. Amu and Co. basically helped create a soul crushing machine.
 * And on that, Kamijou is a descendant of the Tsukiyomi family. Perhaps Tadase too. Perhaps Madoka is related to the Hinamori family, simply because of the pink hair and Annoying Younger Sibling factors.

Goddess Madoka is the latest Elder God before/after Kurou and Al, and Kyubei is an avatar of Nyarlathotep.
Well, Kyubei's race gave human technology and magic, didn't they....

Elly is the witch form of Hatsune Miku.
Compare Elly's human silhouette with Miku. Note the turquoise color scheme, the reddish tint of Elly's hair ribbons, and what look like Miku-ish sleeves on Elly. Many of the speculations on this page of the Madoka wiki could apply to Miku, particularly the part about wishing for popularity as an idol. Her somewhat robotic-looking familiars may refer to the Vocaloids, who are androids.
 * Or she could be Zatsune Miku instead; Elly's witch appearance has black hair rather than turquoise, and Zatsune Miku's hair is sometimes depicted as somewhat shorter then Miku's, which more closely matches the length of Elly's pigtails.

Gretchen's Barrier is Equestria
Well, it is "paradise."

Males who are contacted by Kyubey become Dragonborn or powerful saints and champions.
Kyubey states that the most efficient sources of energy are adolescent girls, but rarely, a male demonstrates a sufficient level of emotional turmoil that they are selected by Kyube to be granted a wish. All of these wishes, by virtue of the extreme emotional distress required to be chosen, involve leaving their own life, and going somewhere else, anywhere else. With this in mind, the men who make these wishes are transported to Nirn, another dimension that is not bound by quite the same laws as our own, due to the presence of gods(The Nine Divines, Daedra, etc.).

Once there, Kyubey erases their memories of their previous life, and plops them down in the middle of the hero fantasy many young men dream of:lets go slay some dragons/evil demon monsters! Their Soul Gems are preserved inside of them, which gives them immense durability and potential over the normal person, but limits their ability to call on its power in the ways that magical girls do. Slaying Daedra allows the Magical Dudes to absorb their energy, which is internalized as their expertise, and sometimes bound into Soul Gems(of the Elder Scrolls variety). By capturing their essence, Kyubey gains energy from the endless font of energy that is Oblivion. Dragonborn, on the other hand, harvest Dragon Souls, which naturally contain immense amounts of power, and gain both power and sustenance from doing so.

From there, a few ends await the Magical Dude. If they fall in battle or reach critical levels of despair, the energy they have collected will leave them, leaving them to become Dragon Priests, Liches, and other undead, which are then hunted by others for their own power. If they get tremendously powerful, without dying or succumbing to despair, they become immensely powerful beings in their own right, ascending to become Daedra(Hero of Kvatch), god-entities(Tribunal, Nerevar), or one of the Divines(Tiber Septim). The energy released in these events, which are similar to Madoka's wish, on a smaller scale, are called Dragon Breaks, to explain the changes in reality which occur after them.

The Witches are Selenim

 * Witches create pocket dimensions that represent their psyches ("barriers," "labyrinths"), feed on human misery, and create monstrous familiars to serve them.
 * Selenim are magical spirits that possess human bodies and feed on human emotions like jealousy and faith. When they've hoarded enough lifeforce, they can create pocket dimensions ("kingdoms," "realms") that reflect their psyche. These pocket dimensions are often populated by monstrous creatures that exist to collect more lifeforce.

The entire series does take place in the Instrumentality of Neon Genesis Evangelion, but Homura is a repentant
While the Oedipus father vs. son aspects aspects are stripped off, there are a lot of similarities between Homuhomu and. Both are not-so-stoics whose only (or at least primary) reason to live is companionship with a Messianic Archetype ( and Madoka for Homura), but unfortunately their beloved messiah gets killed off, thus they acquire a pessimistic outlook and are not above being ruthless Machiavellian anti-heroes who are ready to even screw up all creation as a whole just to preserve that person who is their reason to live (Time-travel and an endless recursion of time for Homura, and . Of course, Kyubey could be Seele, the powerful and manipulative utilitarians who once helped them acquire the ability to perform the reality-screwing in the first place, but also managed to be even more of a jerk-ass and on which both of these stoics rebelled against just to get to their loved one.

When Instrumentality took place during End of Evangelion, This leads us to the events of Madoka Magica which takes place inside the Instrumentality version of Purgatory, where thanks to this wish to become The Atoner,  himself is forcefully genderbended (thus stripping him off of his manipulative  tendencies), and has to spend the rest of his/her life in Purgatory trying to protect Madoka, the representation of both. However, as time progresses and as Homuhomu repeats Purgatory everytime she fails, Madoka also continually takes traits from Shinji (massive decrease in confidence, becomes less of a Messiah and more of a wimp), and thus he/she has to make up for everything by protecting that same Shinji-Madoka too just as he tried to protect Madoka.

Haruhi Suzumiya is a Madoka-scale anomaly/god/witch.
Well the concept of the "Closed Space" and "Celestials" might just as well be Witches' barriers and Demons, respectively...

Episode 12 wasn't the first time the system had been rewritten. "Berserk" was the the first universe.
1 The universe is govern by human will. 2 It is a Crapsack World. 3 Certain humans become monsters after crossing the Despair Event Horizon. 4 Anything approaching victory for Gut would involve rewriting the system. This may or may not involve a Cosmic Retcon.

Quit blaming Hitomi and Kamijou for everything...blame Doc Brown and Marty McFly.
Their (and Biff's) screwing around with the space-time continuum (and bumping into their other selves) put considerable strain on space-time (and Homura didn't help). Remember how Marty was also planning to become a musician until he broke his wrist in a peer-pressure induced drag race? When he averted that fateful car crash, the resulting Ripple Effect created the aforementioned crash 26 years later and 6000 miles away that injured Kamijou (and killed Mami's parents), which of course resulted in Sayaka's contract.

To make matters even more sadistic, in the original BTTF timeline, Hitomi's father was killed in that car crash as a boy, while visiting relatives in Hill Valley. One of the survivors became Marty's boss by 2015. He realized the accident was just a case of stupid teenage recklessness and eventually took pity on Marty in his despondent state, hiring him...but he still nursed a bitter grudge which eventually led to his firing Marty when Needles framed him again years later.

Marty's daughter Marleen had contracted at some point for almost the same reasons as Kyoko (wanting to help her struggling family and continually depressed father). She would've become a Witch either when she was busted trying to bust out Marty Jr. in the first timeline, or when her dad was fired.

So...one ruined musical career (and eventual Witchdom) for another. Take your pick.


 * And oh yeah, an Incubator planted the idea for the Flux Capacitor in Doc's head. With human nature being what he knew, he felt humanity was unable to handle the responsibilities inherent in Time Travel...so of course it would eventually prove a great way to trigger some contracts and harvest some souls.

Walpurgisnacht is Meg Griffin's Witch form.
She lasted about 30 minutes before witching out.
 * For contracting with her, Kyubey got a 50-cent wage increase, one day's paid vacation time and bathroom breaks. (Yeah, it's a pretty lousy workplace, but it's pretty much the only career option on his planet.)

Gen Urobuchi is actually a pen name for Nozomu Itoshiki.
Thinks all wishes and being a timid Nice Girl will only destroy you and your loved ones in the end? Thinks the only way to make the world a better place is by removing yourself from it? Thinks Happy Endings contradict the laws of nature? Yeah, sounds like a certain neurotic, suicidal teacher.
 * The story was originally submitted to his class as a required-reading doujin. The reason the series ended in May 2012 and Studio Shaft has no current plans to animate the end is because his students all committed suicide. Even Kafuka.

Many of the "ghosts" in Ghostbusters Part 1 were actually Witches.

 * A lot of them looked a lot more like Eldritch Abominations than normal human spirits. The creation of Witches gnaws away at the boundary between the mortal and spiritual realms each time it happens (and Doc, Marty and Homura's aforementioned meddling with time didn't help). And then of course that one apartment building was a continually building strain. (It may have been designed under the influence of a Witch's Kiss.) Then one day in the summer of 1984 one unknown fallen Puella became a Wafer-Thin Mint that allowed Gozer and his minions a huge hole to crawl through into our world.
 * Slimer may have an origin story similar to Charlotte (e.g., she suffered either from cancer, diabetes or bulemia). Heck, let's say that she was the straw that broke the camel's back and tore open Gozer's doorway.
 * Instead of giving them the Mercy Kill that our beloved five do, the Ghostbusters of course imprison the Witches in an unstable nuclear holding pen. Wrap your heads around that one...
 * Part 2 takes place after Madoka's apotheosis. That pink slime in the New York sewers is materialized curses. (In the modified timeline, there were still enough troubles with "normal" ghosts to justify the Ghostbusters' business.

Madoka takes place after Instrumentality.
Humanity returned to form from the Tang and rebuilt its society...however, their capacity for arrogance, pride, bastardry and schadenfreude remained, creating Madoka's cruel world where idealism and belief in man's better nature only ever comes at a horrible cost.
 * The Incubators may actually be manifestations of humanity's collective opportunism. And then in most of the timelines we saw, Madoka's Witch form bascially restarts Instrumentality, much like God's intent to destroy the world again in Revelations. "As a dog returneth to his vomit..."
 * About the Incubators being manifestations of our opportunism (as well as sociopathy), Kyubey's talk about aliens and entropy was symptomatic of our tendency to justify our actions with little white lies whenever we "use" people. In other words, we are all Kyubey at times. Or rather, we gave birth to him.

Madoka takes place in the same universe as Bleach.
Both series feature abominations, born from the corruption of a human soul, with names different from their human ones. Kyubey indirectly confirms that Muggles have souls, too. When a Muggle dies, either a) they have no regrets and become a wandering soul until a shinigami sends them to Soul Society, or b) they have regrets binding them to the World of the Living, and they eventually become a Hollow. What Kyubey does is pull out the soul, "killing" the subject, A Wizard Did It preventing Hollowfication and allowing the soul to function outside the body. However, souls were never meant to exist outside the body, and eventually, even Magical Girls Hollowfy, the magical alterations of the souls causing the Hollow to become a Witch - a Hollow with magical, Reality Warping powers. This would also mean that Witches become stronger by consuming one another or by fusing, which would explaing Walpurgisnacht.

Misc (Odd stuff, symbolism, meta concepts, etc etc)
Anything not directly story related, and/or things we'll never be able to confirm.

Madoka broadcast will skip one week to make series end on April 30 instead of 24.
In Madoka the big finale will happen on Walpurgis Night. And Walpurgis Night is April 30.
 * They might be able to make a 13th episode or do the same thing like what they did to Bakemonogatari.
 * CONFIRMED.
 * Except that this puts the probably end-date at March 31.
 * Yeah, the series is supposed to end in March, not April. Speaking of which, due to timezones it might be April 1st in Japan when it airs. April Fools? Keeping it in Meta because they might release a bonus episode on April 30th, who knows?
 * Very unlikely, but since episode 11 was delayed again...
 * If they delay the final episode until the Walpurgis Night I will be scared. Coincidence, yeah right.
 * It's going to air April 21. It's...pretty close.
 * It aired on Good Friday 2011. Madoka Died For Your Sins!

The whole series is an experiment
Specifically, an experiment on writing a show based on internet theories. They started out with character designs and a general concept and direction, dropped hints that it would be an extremely dark show (the leak about Urobuchi Gen's involvment was no accident), and then let the theorists go to town. They keep a close eye on all the forums and wikis that are examining the show, take the theories they like best, and use them. Heck, just look at all the theories that have been confirmed/lent credence, from this page alone!:


 * Kyuubey really might be evil (this was one of the very first theories here, appearing shortly after the first episode aired).
 * Witches are.
 * Sayaka becomes a.
 * Homura is a Time Lor- I mean Traveler, of all things (Another episode 1 theory).

After all, what better resource is there than the audience's imagination?

A popular 4 koma gag comic in Japan's internet community involves QB as a used car salesman, desperately trying to get people to sign up for contracts because his bosses are on him to meet his quota. In episode 10, one of the things he specifically mentions is that  Uh...

Has anyone noticed...
...that Madoka's necklace in the main page artwork bears a striking resemblance to Kyouko's soul gem? Thats a whole other Epileptic Tree right there...
 * It Gets Worse. Look at this (Ads NSFW) It would certainly make all the Kyubee and Madoka hate Hilarious in Hindsight...or the opposite

Each magical girl is a representative of another magical girl show
Not an outright expy, but more of a conglomeration and may or may not be corrupted somehow. For example, Kyouko Sakura says this to Sayaka: "I told you and I hit you, but you still don't get it", and before that tells her to take a chill pill. This is pretty much Nanoha's Modus Operandi. On a more superficial level, she also wields a pole-arm, which can break into chain-connected segments simultaneously bearing similarities to Raising Heart and Levantine.
 * I can see it happening... But not only to a series. To many of them, perhaps.
 * Mami: Might be Kamikaze Kaitou Jeanne, although one could say she took the "Kamikaze" part a little too literally.
 * Sayaka: Magic Knight Rayearth, perhaps? Has the whole sword wielding thing, not to mention the "I can't be with my beloved one" part...
 * Homura: Sailor Moon, perhaps . And maybe a bit of Zakuro's personality,.
 * Kyoko: As you said, Nanoha. And maybe a bit of Saint Tail as well (even the clothes are a bit similar, not to mention the whole Catholic thing going on).
 * Madoka: A reversed Cardcaptor Sakura (Sakura must be a magical girl to prevent a terrible thing; Madoka must not become one to do so). Not to mention that I couldn't be the only one to see similarities between her clothes and the ones Sakura uses in all openings.
 * Oriko and Kirika: The one in black is the one that fights while the one in white is the one who sits in the sidelines. This fighting style is pretty much like Futari wa Pretty Cure.
 * Kirika's last name is Kure, which contributes to this hypothesis.
 * Kazumi: Sugar Sugar Rune. She has a Cute Witch magical girl outfit and a food motif.
 * Kazumi: Sugar Sugar Rune. She has a Cute Witch magical girl outfit and a food motif.

Conversely, all witches who appear are representing girls from different animes.
Said animes being not necessarily in the mahou shoujo genre.
 * Charlotte is related to Cartoon Network, I believe.
 * Specifically Foster's Home for Imaginary Friends. Tell me her second from doesn't look like an Imaginary Friend.

Puella Magi Madoka Magica takes place before every Magical Girl show ever.
Originally, every magical girl contract in every universe was a Deal with the Devil - it only makes sense for Madoka's story to have to take place before all of them. Also reinforces the "Madoka = Jesus/Goddess of Magical Girls" concept.

The random corruption in the Cypher Language isn't random.
The cypher language has random errors in it, possibly to make reading it harder. Or, perhaps, it's a longer message that's playing out through the episodes, designed to be read at the end.

Someone will give Kyubey a "The Reason You Suck" Speech.
Don't we all want this to happen? Anyway, in the dream at the start of the series, Madoka gives Kyubey an angry/determined look just before it ends. If the WMG that she won't accept a contract is true, she may be gearing up to deliver one of these.

The series will eventually be followed with a Reconstruction of the Magical Girl genre.
People have compared this to Neon Genesis Evangelion so much, it's only natural that we'll some day see its Gurren Lagann. And while the genre has been deconstructed several times before, to my knowledge there's never been a reconstruction, at least one popular enough to be widely known.
 * Perhaps the second season of Panty and Stocking With Garterbelt? Or perhaps a Sailor Moon remake? It has to be tons of badass, either way.
 * Sort of confirmed, since Madoka reconstructs the world so that despair now forms demons instead of turning girls into Witches. The sequence is even somewhat similar to the Third Impact sequence from End of Evangelion.

Madoka Magica is an Allegory of Drug Addiction
A little guy comes and offers the girls an offer of a great pleasure. The catch is, once they are in, they can't get out, with death being the only apparent exit. They also need to constantly find these "Grief Seeds" to survive. They fight each other to obtain them. Not to mention that when in the proccess of extracting these "seeds" they find themselves in such a bizarre space (or state of consciousness).

Homuhomu, an already addict, comes and tries to warn Madoka about not getting into it if she cares about her life and family. Some think it is because this would reduce the amount of narcotics she can acquire, but maybe it is really because she doesn't want others to suffer her same fate. She tries to shoot down the dealer, Kyubey, before it's too late. But the girls find him and get interested in the thing after a little try. They meet Mami, a "veteran" in this and tries to turn them in as well. She started consuming them because she "had no choice", she had no family, she was alone and depressed. It "saved her life". What was the result of having this way of life for so long? .

Horrified, the girls doubt. But Sayaka, who has her own problems, becomes more and more interested. Kyubey is constantly trying to make Madoka turn in; as to what the potential about her he is talking about means, I'm not really sure yet. When Kyouko comes, she is not really interested in stopping the death of the innocent lives all the narcotrafic or the drugs themselves cause. More for her.

However, later they find out just how much these things deteriorate their bodies, to the point of in episode 6, and even she is disturbed. Sayaka. They really can't go on without it.

So, maybe now you will think differently next time you see these girls "fighting witches".
 * THIS.
 * Check out the Poison Oak Epileptic Trees "Madoka is one giant drug trip." Kyubey is a pale, balding Ephebophile with red eyes.

The witch in episode 4...
Is the female populace of our community not even safe? The witch was saying phrases like "she don't like fools" and "I'm young so I will not work! I will only live, live, live!" Also notice the form: ITS A COMPUTER MONITOR FROM THE 90's! Poor troper got herself turned into a witch... DAMN you EVIL WHITE RAT!
 * Oh and apparently her name MIGHT be "Elly Kirsten"
 * Confirmed, I guess, according to the cards, Elly is Hikkimori witch.

Kyubey works on commission.
Have you ever tried to buy or lease a car? They can get REALLY pushy. Also, with Homura following him around, he's probably really hurtin' for new contracts.

Madoka's wish will restore everything to normal to before they met Kyubei
OPTIONAL: However it will go horribly wrong.

Each witch is an Allegory of the Seven Deadly Sins.
It is now known that witches are born from negative emotions. Perhaps the form they take as a witch is based on their greatest sin.
 * Gertrud represents either Pride or Lust
 * Charlotte represents Gluttony.
 * Elly represents Sloth
 * Elsa Maria represents Pride or Wrath
 * Since the was supposed to represent lust, perhaps  is lust and Gertrud pride?
 * Since the was supposed to represent lust, perhaps  is lust and Gertrud pride?

Kyubey tastes like marshmallows
You know you want it to be true.
 * Confirmed?

Morning Rescue...
Will break the Walls of Reality and rescue Madoka and everyone else. Then everyone will enjoy a nice cold glass of LCL.
 * Confirmed?

All the confirmed Wild Mass Guessing in this page were written by people who made a contract with QB
/人◕ ‿‿ ◕人\

QB is a wife-/mate-beater.
... Yeah, I know this is kinda Dude, Not Funny, but I Always Wanted to Say That "Wishes? You know who gives wishes? Blokes what bludgeon their wives to death with a golf trophy."

It's all planned by a really sadistic cosmic being.
Kyubei is just a vessel for it.

Urobuchi being the writer was a Red Herring
So that nobody would notice the real one. The real writer will be revealed to be Ryukishi07, and the plot was caused by Bernkastel's boredom as a WMG above mentioned.

Japan's 9.0 magnitude earthquake was caused by the coming of the Walpurgis Night
Madoka's power is enough to Punch Reality
 * Confirmed by Word of God?
 * Too Soon, man.
 * You should stay away from /a/, then. It's even parts this joke, Tokyo Magnitude 8.0 jokes, and complaints about how earthquake reports are going to fill the screen for the rest of the season.
 * Alternatively, caused by Homura in some desperate attempt to stave off the inevitable.

Gen Urobuchi is an Incubator
In a similar vein, Puella Magi Madoka Magica is an extremely efficient emotional energy collection mechanism. Why spend the effort to draw energy from a couple of little girls at a time, when you can get energy from a much wider range through television? The reason why he tried to hide his involvement was just to heighten the hope we'd all feel to boost the effects of the slow dive into despair.
 * It all makes sense now! It all makes sense!
 * It goes further. He harvests the disproportionate nerdrage that results from his trolling. One simple anime spawns a massive fan effort that generates more emotions and even more nerdrage in a cascade of entropy-defying disproportionate reactions, thus ensuring that he won't even need to really make little girls suffer when a cascading avalanche of fan reactions produces infinitely more efficient energy. Now that is true genius.

Kyuubei is Maxwell's Demon.
What if you could summon a demon to negate entropy?

Homura is an AU Ghost Rider.
If QB is Mephisto...
 * or you know, Faust.
 * Given that Madoka's Witch form is Gretchen, the name of the woman Mephisto tries to get Faust to corrupt; it's apparently Homura who is Faust.

There will be an AMV of "Friends on the Other Side".
Listen to it! Doesn't it fit Kyubey?
 * You want a song that fits Kyubey? Poor Unfortunate Souls.

The staff will end up releasing episode 11 in late March, and episode 12 on April 1.
Then they get an excuse to make some weird Gainax Ending and say "Haha! April Fools'!"
 * With no episode 11 in sight, I believe this one is Jossed at this point.

Episodes 11 and 12, and the ending of Madoka altogether, will be Bowdlerized.
As to not offend victims of the Earthquake & Tsunami in Japan. This would explain the delay of Episodes 11 and 12. Even if they aren't Bowdlerized by SHAFT, they still could be watered down by the stations broadcasting Madoka.
 * Semi-confirmed in that this was why the delay kept getting extended: the channels refused to broadcast something of that nature. Either they've gotten around it, or they Bowdlerized it (but chances are the Nico broadcast will probably be untouched).

Fans will be dissapointed by the finale

 * Jossed, thankfully. By and large, the finale was very well-received.

Urobuchi is Kyubey and he is trying to
Or rather, Kyubey, entropy, and the entire despair-powered Cosmic Horror Story universe are projections of the "tragedy syndrome" from Urobuchi's afterword of Fate/Zero from which Magica draws from. He is the part of himself that was taken over by the pessimistic-yet-realistic "Silly Rabbit, Idealism Is for Kids" philosophy, making him no longer comprehend happy endings and become a bearer of the plague to his worlds. But while creating some of the darkest scenarios possible, he is also littering them with the means to turn things around. Not easily or without things worsening first, which is why Homura, who can represent his "true Self" trapped between hope and despair, has the ability to.

Mami's wish was likely. Kyouko's was to. With each attempt, Madoka's Homura has yet to completely outgrow being a  Possibly through a wish as simple as

With Episode 12, aka Urobuchi's happiest ending, this guess might just be likely.

Or these are all hope spots for the audience.

The broadcast delay was done to re-animate the first section of episode 11.
During the 2011 Tōhoku earthquake, some of the creators of the show tweeted "It's Walpurgis Niiight~!" and such, suggesting in-show that the appearance of the Walpurgis would cause some sort of earthquake. This would also explain why the official explaination for the delay was "self-restraint" -- they realised it would be very cheap of them to use a massive earthquake in light of the tragedy and the first half of episode 11 was re-animated to be a storm rather than a quake.

Madoka Magica promotes the use of clean, renewable energy sources.
Think about it for a second.

Gen, you Magnificent Bastard! Everything has gone exactly as you planned!
 * It's funny, I came to this page exactly to add this. Goddammit, that makes this theory look more true...
 * What makes this even better is the windmills contrasting with the oil rigs in and around the city. Alternative energy was the theme the entire time.

Homura saves Amy
As a reflection of what Madoka means to her, Homura saves Amy, in spite of everything else going on.

The Incubators were created by the Reapers.
If we take Episode 11 into account that Incubator helps humanity to advance (for the Reapers to harvest them).

Commander Video is Homura in the far... far... future.
In the far... far... future end of the universe as we know it where the universe turned into 8-bit, Homura is still alive... searching... for something... Her purpose is unclear due to how the universe changes.]]

When Homura dies/disappears...
She will Ascend to a Higher Plane of Existence with Madoka, and be together forever.

May 21st was going to be the end of the world...
...but then a bunch of Puella Magi prevented it from happening.

IN AMERICA! Kyuubey turns you into lich.
In Soviet Russia, lich turns you into KYUUBEY!

Madoka and Homura form two "human/flawed" parts of one Jesus
Well with all the Madokamists preaching Madoka as our Saviour we didn't notice that Homuhomu is always there protecting Madoka even if it means bearing the eternal torment of an endless recursion of time, and isn't that like something Jesus would do for your salvation? Initially in the original timeline Madoka is a full-blown messiah who suffers for Homuhomu. When Homuhomu wished for Time Lord powers to protect Madoka, in other timelines (like the series timeline) she suffers for Madoka, making Madoka gain the power of multiple universes revolving around her and making her think about what she really wants to wish. In the end Madokami is able to suffer and die for everyone's sins, bearing the eternal torment of the world's despair upon her to prevent witches from happening, and in the new witch-free timeline that she created, Homuhomu protects.
 * Jesus is when Homuhomu's sacrifice is combined with Madoka's agape.
 * Alternatively, Everyone Is Jesus in Purgatory, and Kyubey is the Devil/Demiurge.

The series is based to a measure on Valentinian Gnosticism.
First, a bit of clarification. Gnostic schools like Valentinianism, while still somewhat suspicious of the physical world, did not go so far as to declare it innately and irrevocably monstrous. We're at the other end of the Gnostic scale from The Second Treatise of the Great Seth.

The PSP game has an interesting witch in the last Bonus Dungeon:. While this really could just be honoring  through , it does bring up an interesting thought, that the Incubators themselves are a composite familiar, or at least very much akin to such. Thus, their creator/liege is like unto a witch. And so begins the train of thought...

Unlike schools that regard the Demiurge as a simple Complete Monster, Valentinianism thinks of him as more of a misguided Lawful Neutral who is obsessed with rules and stability. The problem is that his methods of keeping the flawed physical creation together generate plenty of grief and woe fallout for the mortal denizens. The archons, his police force, don't really help the situation. It helps to look at the more severe schools, where the archons torment and harass mortals for their own amusement and edification...and sometimes, their sustenance. While the Demiurge is still well-intentioned, that (somewhat alien) benevolence is nonetheless malign for certain denizens. Then again, the Demiurge seems to be more concerned with the physical universe as a whole, and himself and his archons whose eternal dwelling it is, than the self-aware subset.

So basically, we have a creator and angels who can't see the forest for the trees. Stabilization at the cost of sorrow isn't that good a trade! However, Valentinianism also posits that the aeons sent a Messiah (variously the Serpent of Eden, Jesus, etc.) to help redeem the creation from the Demiurge's mismanagement. Unlike the view of the producers of the Second Treatise, though, the Demiurge and his archons are meant to be redeemed as well. Also important to consider is that in at least most schools of Gnosticism, human souls are actually divine sparks that got unwittingly trapped in the physical creation as the Demiurge produced it. The Demiurge, mind you, has no real idea that the souls are divine in nature; he's just wholly ignorant of the existence of anything outside himself and his creation (the aeons are working on that, though). So, because they're not archons, he has no way to see them as important unto themselves, as being mini-aeons would imply—he's Obliviously Evil. So, in short, he's busy keeping the world going as he's always done, no matter how much woe is produced as a side effect, because he literally has no ability or cause to imagine a Plan B at this time. He just doesn't know how to care. The Messiah is here to get Plan B going, whether the Demiurge initially approves or not.

Mapping to Madoka...The Incubators are, if not the Demiurge, then his archons. They manipulate the divine-sparked mortals (specifically, potential magical girls) to harness what's needed to keep creation as it's "always" been. While the magical girl/witch cycle can seem like sadistic schemes for the Incubators' amusement, it's really "just" the only good way the archons can think of to keep things going (not that it makes the situation less malign, that it's not actively malevolent). The amount of high-grade (they don't know it's actually divine/pneumatic) energy they get results in universe-wide stabilization that outmasses the Earth-localized rue. And are the magical girls ever manipulated—they practically become unwitting archons...

However, because of Homura's persistence, Madoka understands not only the true nature of the Incubators' schemes, but also that they're genuinely trying to do the right thing. Their understanding of right and wrong is, like the spirit-ignorant Demiurge's, incomplete. Homura, like the untiring Messiah throughout his/her many incarnations, has awakened Madoka, the representative divine spark, to the truth/gnosis. Only the Incubators' mechanism is bad; the goal isn't. And so, by taking the Messiah mantle herself from Homura, Madoka commences the salvation of the system. It's not complete, not by a long stretch, but at least this way, the manipulated magical girls are instead released into the Pneuma after they've done all they can, rather than become victims of Demiurgic foolishness—just as those who know the truth (as, after Madoka's work, they do as a matter of course) can reach salvation rather than stay stuck in the Hylic/physical mire. And given enough time, perhaps the archons/Incubators, too, will figure out a way to stabilize/save the universe that doesn't require energy harvesting from innocent mortals...

The series is a metaphor for the Seiyuu and pop idol industries, and by extension how Music Is Politics and Hollywood is evil in general.
Aya Hirano and Michael Jackson are certainly testimonies to the chew-'em-up-and-spit-'em-out nature of the entertainment industry. Also noteworthy is how so many young modern seiyuus and artists (wait for it...) signed the contract because they were fans of Sailor Moon or other cheerful TV shows, only to discover that they get most of the downsides of celebrity life (Typecasting, Slave to PR, Artist Disillusionment, being virtually whored out all the time by Corrupt Corporate Executives who always desecrate their Magnum Opus, creepy stalker fans, having to keep their private/romantic lives complete secrets to avoid eternal damnation by the Fan Dumb, not even being able to avoid said eternal damnation due to accusations about scandals...) with very few of the perks (seiyuus go into idoldom and gravure shots because voice acting actually does not pay too well in Japan, and most idols themselves only get judged by their cover and not their true self).

You may know already that even if you're a rich popular celebrity you will still be able to fall into Despair Event Horizon (hence reckless hedonism or suicide), and are in fact more susceptible to it, but most people may never notice because of the "all kinds of fame=money=anything you want" imagery. What's worse is that when you do fall into Despair Event Horizon the executives will whore you out even more (paparazzi, Dead Artists Are Better, etc.) thus more money for them, and they don't even have to pay you back since there will be more suckers who want to emulate your fame and wealth (this parallels how Incubators extract even more energy from magical girls falling to Despair Event Horizon and turning into witches, which in turn creates increasing demand for more willing magical girls to outshine said witches). Just like how if you're a Magical Girl you can get anything you want, and everyone sees you as a hero, but unfortunately deep down you're just a zombie who's reduced into nothing more than a glorified furniture of the Incubators. Also, according to Music Is Politics:

"Younger artists are very susceptible to this trope. This is probably one of the reasons labels prefer younger artists: they're less well-versed in the ways of the business and easier to control. And it's likely the reason the industry focus on younger listeners. Older music buyers/listeners already know what they like and don't like, where as younger listeners can betoldwhat to like."

Sounds like why Kyubey prefers making liches out of young, weak, unknowing, diabetes-tasting girls with high hopes (like Madoka and Moemura) instead of the older more strong-willed ones experienced in business (like Junko), right?

The Eldritch Horror behind all the Madokamisery and the Entropy is..... TV Tropes!
Where did Entropy get its name from? The prefix "en-" coupled with of all things, the word "TROPE". Kyubey requires making a Deal with the Devil to sustain the universe. TV Tropes requires ruining your own life to sustain itself. Makes sense?
 * It wouldn't be wild to even speculate how Urobutcher is one of those ruined lives.

It's all a financial metaphor
Contracts = loans. Homura trying to rewind time only to make Madoka an even more destructive witch = Trying to get out of debt only to end up increasing the interest and in even more debt.

So Gen Urobuchi and Hideaki Anno walk into a bar...
...and seven drinks after the bartender tells them there's a five-drink minimum for setting up bad Dead Baby Comedy jokes, Urobuchi makes a bet to Anno and the bartender that he can beat Anno at making THE most depressing anime ever.
 * Gen never got his money from the bartender, since he had committed suicide.

From the aforementioned Evangelion WMG; the Incubators are actually manifestations of humanity's collective opportunism and sociopathy under a mask of civilization.
With the rise of agriculture/industrialism, establishment of cities, increasingly stratified societies, and insatiable mass consumerism, humanity's capacity for empathy decreased, while raw sociopathy, opportunism, greed and ambition built up to critical mass. Today, idealistic themes we saw all the time in Magical Girl shows, such as The Power of Love, are nothing more than a marketing ploy for the dominant ruler of the world, The Power Of Love For Material Wealth.

All that stuff about aliens and entropy is symptomatic of our tendency to justify them with little white lies and Half Truths whenever we devastate nature or take advantage of our fellow man. It took the form of a race of seemingly harmless RidiculouslyCuteCritters for much the same reason; we all try to convince ourselves we're right, we're just trying to help, and the destruction of the earth is all for the sake of Enlightenment. In other words, we are all Kyubey. Or rather, we are all his/her/its/shkler father/mother. Search your feelings, you know it to be true.

Also, when Madoka asked what would happen if Kyubey never existed, Kyubey replied that humanity will still be naked living in caves. Thus, Kyubey's Industrialized Evil is presented as something good and necessary. Unfortunate Implications arise when "bringing civilization" is also one of the reasons the Europeans justified slavery and destruction of tribal cultures.

"You have some really great ideas. I can make any of them true. All I need is for you to make a contract."

- /人◕ ‿‿ ◕人\