The Phantom Menace/WMG

Darth Maul is Emperor Palpatine's clone.
Sidious was a patient man, but he was a Sith, and Sith, by their very nature, want to be Drunk On the Dark Side. He wanted to take out Jedi, but he quite obviously couldn't show himself to the Jedi just yet. So he reconciled his bloodlust by cloning himself and adding super-cool makeup (i.e. horns, tattoos). If you accept the Expanded Universe as canon, this would be in character, as in the EU, Palpatine created LOTS of clones of himself. As a bonus side effect, the resulting clone would look like a Zabrak, eliminating any human resemblance. Maul also used a double lightsaber, giving further proof that Maul was a Palpatine clone- no sane being would use such a dangerous weapon. But Palpatine/Sidious had his own body,and did not care if another clone died.

Midichlorians are a species of microscopic Mushi that allow manipulation of the Life Stream.
Really, with all the various Mushi running around granting Blessed With Suck superpowers to their hosts it's pretty obvious.

There was no Darth Maul.
Think about it. He had no impact on the events of Episode I other than killing Qui-Gon. And Obi-Wan was the only surviving eyewitness of that fight. It was explicitly stated that Qui-Gon was disobedient of the Jedi Council. So, obviously, the Council had Obi-Wan assassinate Qui-Gon when his back was turned. Fast-forward to Episode III. Obi-Wan, despite being noticably younger than the other masters, is on the Jedi Council. Why? Because he removed a thorn from their side. Everything about Maul in TPM was just apocrypha or Jedi propaganda. But what about that throwaway line about Qui-Gon teaching Obi-Wan about Force ghosts, you say? Yoda already knew the technique and had taught it to Obi-Wan, and the line was just part of their cover. It must not have been to hard to learn once you had the idea, since Vader apparently knew it in Episode VI. Besides, if the prequels are any indication, Palpatine burned through apprentices at a rate no other Sith Lord could dream of. What's one more or one less?
 * In the Expanded Universe, Maul left at least one reliable living witness: "In 0 BBY, Darth Vader encountered and defeated a clone or doppleg&Atilde;&curren;nger of Maul created by the Secret Order of the Empire, possibly under orders from Palpatine." However: Clone? Doppleganger? This smacks of a setup.
 * And in the movie, Anakin and everyone in the cockpit of Amidala's ship saw Qui-Gon's first fight with Maul. Then Padme and a large number of soldiers saw Maul in the palace on Naboo, before the lightsaber fight started. If this mysterious black-robed figure was not really a Sith, he was a good enough impersonation of a Sith to fool Qui-Gon.
 * Maul was like Asaji Ventress, just a random moron that thought he was a Sith. Sidious just used him as a tool.
 * Wrong. Maul was a full fledged Sith Lord despite his tendency to act like a stupid wild dog. He was Palpatine's first apprentice, and the one who he trained from birth.
 * The clue's in the name: Maul mas intended as a blunt object to use against Sidious' enemies, never intended to be his successor. The man does tend to burn through the apprentices in these movies.
 * All of them he viewed merely as pawns in his plan to convert Anakin to the Sith. He had been plotting to take Anakin as his apprentice since before he killed Darth Plagueis (who had created Anakin to replace Palpatine as his apprentice)
 * I'd buy this if Maul hadn't also been witnessed in the Theed hangar by the Queen and her entourage, as well as Anakin. Not to mention Sidious and the Neimoidians also saw and interacted with him.
 * Well, how about this: Darth Maul was real, but was Sidious' fall guy, whose unbeknownst purpose was to distract the Jedi from Sidious himself. Unbeknownst to Sidious, he also became the scrapegoat for Qui-Gon's slaying. After the two Jedi killed him, Obi-Wan took out Qui-Gon, and even had a cover-up to pin it on.

The Force attracts Midichlorians.
Taken from the Star Wars Technical Commentaries, source of the Endor Holocaust theory. Alternatively, increased Force sensitivity and Midichlorian presence are caused by some other factor, but have nothing else to do with each other. Jedi use Midichlorians count to measure Force potential because of the correlation, not a cause-and-effect relationship. Midichlorians are just benign microorganisms, possibly ones drawn to the Force, that do nothing else.

Alternately, the Force creates midichlorians.
It's a side-effect of using the Force, which rearranges organic molecules into certain patterns inside the Force-using organism. This would explain why the exact same subcellular organelles could be found in completely unrelated lifeforms who evolved on different planets.
 * According to Wookieepedia that's the Jedi theory!
 * WP is a fan Wiki, don't forget. The popular theories get on it, not guaranteed Canon.

The people of Naboo were really brutal to the Gungans
This is why the Gungans were so hostile towards the surface society - the humans liked to harass and torment them. There were even pogroms against them, now and then. Padme wasn't horrified by Anakin's slaughter of Sand People because slaughtering some non-humans who'd wronged a human didn't strike her as that bad.
 * Since Palpatine is from Naboo, this would also explain why The Empire is so xenophobic in the Expanded Universe.
 * After having seen the Gungans, who WOULDN'T want to commit mass genocide against non-human creatures?

Midichlorians are actually a unit of measurement, like... oh, say, a Rad or something.
Thus, when they're talking about Midichlorian counts, they're basically waving a Jedi Geiger-counter at the subject and seeing how much Force radiation he's emitting.
 * I figured it was a count of active midichlorines. Inactive, they aren't detectable. They're a dormant "junk DNA." Activate them, and that's when the problems start. Worse, they're present in everyone. Some of them are active at birth, some get activated later on through accident or direct intervention. This makes Force Sensitivity a much more common trait than either saber-swinging faction will ever admit to - the Sith wouldn't bully the sheep with impunity if they could fight back, and the Jedi would fear that the rabble wouldn't have enough sense not to abuse it. When times are good, both factions can cherry pick among recruits they can best control. When times are bad, they make do with what they have. This is how Exile and Luke were able to assemble and train a fair amount of Force users in a relatively short time, and how Revan could get Dark Jedi on every damn street corner during the Jedi Civil War.

Midichlorians are an organ existing in the body of Force-Sensitive species.
They aren't microbes independent of the body, but a part of a creature's own physiology; a network of cells that allows a living creature to interact with the force.
 * Like an extra lining for the liver?

This is why, for example, force ability can be passed to children. Then there's the "Midichlorian Count" thing. A body's Midichlorian System can be stronger/weaker innately, just as different people have stronger/weaker eyesight. Or it can be strengthened with use, like a muscle, which is why trained force-users are so strong, they exercise and hone their Midichlorian System until they can use lots of Force at one time.

The story of Episode 1: The Phantom Menace was at least partially inspired by Spaceballs.
I know this theory sounds somewhat off because Spaceballs itself was a parody of the original three Star Wars movies (and their merchandising), but considering the storyline, there are some striking resemblances to Episode 1: The Phantom Menace. Both films begin with an idyllic world of peaceful people who is attacked by bureaucratic morons with superior techology. Eventually, the heroes of the film enter the scene and rescue an important female member of the Royalty of the attacked planet from the attackers who want to capture her. However, they are forced to ditch on a desert planet, where they get some help from the natural inhabitants. Then, after a short visit to the home planet of the Big Bad, they return to the princess' planet just in time to save it from the attackers. If you consider all this, it's not completely out of the realm of possibility that George Lucas got some inspiration from the parody.

The bad guys are the "Trade Federation" and they are repeatedly referred to as "The Federation."
Anyone else think this is a subtle jab at Star Trek?
 * What do you mean "subtle"?

The "baseless" accusations against Valorum secretly came from Palpatine.
This is Mr. Everything That Has Transpired Has Done So According To My Design we're talking about it -- you think there was any part of his scheme he didn't plan? He just let a scandalous rumor about Valorum into the grapevine and then just sat back and watched him be weakened.

This is canon. It is detailed in Cloak of Deception.

Midichlorians are a specific variety of Mitochondria.
Specifically, Mitochondria let you enjoy delicious oxygen, Midichlorians let you enjoy delicious... the Force.
 * Wait... then A Wind in the Door is set in the Star Wars universe? Are you saying Charles Murry and Proginoskes are Jedi?

Alternative Character Interpretation: Qui-Gon Jinn is one sketchy mother who has no business screwing around with any young’un’s life, much less galactic intrigue.
Qui-Gon Jinn is the Phantom Menace. He endangers the Republic, or rather the entire galaxy by just not having a coherent plan--or coherent anything. “Sure, okay,” you might say. “Fans like to pile on him for inadvertently setting the whole Empire thing in motion, and vouching for Anakin so that the Council would agree to his training.” The WMG is in this: If you analyze his actions in a critical light, it had to be intentional! He spends most of Episode 1 being totally feckless, using such questionable actions such as attempting to use the Force instead of diplomacy and explaining realistic-sounding plans to get through situations, staking the mission on an insane gamble with the pod race, bringing the kid to a war zone... oh, just watch the video, you’ll see more.

Qui-Gon Jinn is a terrible Jedi, both in practice and principle.

 * His first line indicates this. They're in the heart of the enemy, and he states that he doesn't sense any danger.
 * He can't use a mind trick on Watto. Watto explains this by saying it doesn't work on him, but how would he know that? It's doubtful he's run into many, or the slavery on Tatooine would probably have been abolished.
 * He senses the Force in Anakin, and tries his damnedest to sell the idea of training him to the Jedi Council. The Council, and even Obi-Wan, insist that this is a horrible idea, either because they don't sense the Force in Anakin because it's not really very strong in him, or Qui-Gon is not in tune enough with the Force to sense Anakin's potential role as a threat.
 * When his Force powers do work correctly, they're usually for corrupt purposes, as indicated in the video linked in the WMG above.
 * That would explain why he's being sent off to unimportant little planets in the ass-end of nowhere rather than being on the Jedi Council.

Anakin was NOT a virgin birth.
Shmi was a slave. Its possible that she was raped/was with someone who she would never would want to tell people about, so told people that he was a virgin birth.
 * Or she just wasn't being literal. One possible translation is: "You're kidding, right? I had the kid inside me for nine freakin' months. His dad took off\was a rapist. Forget him. That kid's mine."
 * She could also be a unique mutation that allows her to have virgin births.
 * Darth Maul
 * Or Anakin's father was a powerful force user who erased Shmi's memory.
 * It was Qui-Gon. That's the real reason he was so interested in Anakin.
 * EU says that Darth Plagus, Sidious's master, used midi-chlorians to create Anakin as the ultimate Sith. And I guess it worked.

Shmi is the most powerful, force-sensitive being in the galaxy history.
(Palpatine mentions that the force can, in some circumstances, create life. He might be lying to get to Anakin, but it might be the truth.) Shmi was a kind, compassionate, reasonable, calm and composed person, just like a Jedi should be. But she was a slave on some backwater dump where no authority could get to her and aid her in developing her talents, and even if they would, the films never show a female human Jedi Knight so it's probable - and likely - that nobody ever bothered with human females having talents. But as she lived her lonely, hard life on Tatooine, she wished more and more for something positive in her life, and so subconsciously she used the force to get herself pregnant.
 * That would an extremely specific prejudice on the part of the Jedi.
 * Furthermore, there are plenty of counterexamples in the Expanded Universe. Or even if you're a movie purist... remember that old lady in the library?

Jar-Jar Binks was the "hero of a thousand faces" in The Phantom Menace.
Think about it: Jar-Jar is the one whose life sucked and who was rescued from certain death by mysterious strangers. He then goes along with the strangers on a voyage where he ends up helping them rescue a princess, gets assigned a ridiculous military rank in spite of having no battle experience, finds the strength within himself, and defeats the bad guys on the field of battle, then gets a heroes' celebration at the end. There's no other explanation. He's also the only character in the film who can be described without use of physical characteristics, wardrobe, job, or actor portraying him.

Padmé is the "hero of a thousand faces" in The Phantom Menace.
No one considers her because she's The Chick, but think about:


 * Refusal of the Call ("I will not condone a course of action that will lead us to war.")
 * Crossing the First Threshold (escape from Naboo)
 * Belly of the Whale (Tatooine)
 * The Shapeshifter: Qui-Gon
 * The Goddess: Anakin
 * Road of Trials (Senate)
 * The Temptress: Palpatine
 * Leave Your Quest Test: Provided by Palpatine
 * Night Sea Voyage/Crossing the Return Threshold (return to Naboo)
 * Ultimate Boon (capturing the viceroy)
 * Freedom to Live (Naboo is free)
 * I am inclined to disagree - She has no real arc. She goes from being the leader of Naboo who sees war as a last course of action to being the leader of Naboo who sees war as a last course of action. Her worldview remains unchanged. She simply realizes that she's already in the middle of a war and acts accordingly. She presumably has had military/tactical training, as could be judged by her sharpshooting and knowledge of merc ops.
 * Her arc is realizing that she's in the middle of a war. Before she thought the system worked and that they could avoid violence, but after seeing the corruption of the Republic, she realized that she had to take matters into her own hands.

Padmé started the Separatist movement.
Padmé declaring no confidence in the leadership of the Republic opened the eyes of many people to the Republic's inability to cope with anything, and they became persuadable to join a certain Count ten years later.

Years on Naboo are much longer than normal.
Padme would actually be in her twenties anywhere else.

Nothing in Star Wars happens after a shot in the end of the Senate scene.
In the movie ET the Extraterrestrial there are many references to the Star Wars throughout. However, in one of the last shots of the senate in The Phantom Menace is a bunch of E.T's species. If Star Wars is fictional in E.T., but E.T. is non-fiction in Star Wars, then Star Wars from that point forward is in a paradox of not being possible, and in the great breach in logic, the series from that point can not exist, and it all is just spiraling out of existence.

Obi-Wan knew about the decoy Queen all along.
Considering all the time they spent together in the ship on Tatooine, he had to have picked up on it through the Force. When Padmé finally reveals herself in the swamp, almost everyone not apart of her security team is shocked. Except Obi-Wan. Qui-Gon obviously detects some sort of "Well, duh. I can't believe this surprise to most of you," feeling from Obi-Wan, cause he gives him a dirty look.

The Phantom Menace is Jar-Jar.
Palpatine's convoluted plan could not have worked without Jar-Jar's seemingly random actions that get the heroes to exactly the right place to maneuver events in the way that best aids his political rise. This continues in the second movie, where his position as Senator was a reward for his service and to position him to grant Palpatine the power of a dictator. This would also explain why Jar-Jar is comparatively dignified in the second and third movies; his behavior in this one was a ruse to make him seem too stupid to pose a threat. This is also why he glomps Qui-Gon as soon as he sees him and then he constantly follows the Jedi around: he was probably following Palpatine's orders to stay close to some Jedi in order to manipualte the events.
 * Also, sometimes he demonstrates to be very coordinated (his agile dive into the water, his handspring when he gets up again after being knocked down). A little too much, for someone who was "banned for being clumsy".

Jar-Jar is a competent Gungan.
...Just extraordinarily clumsy. He was shown to be among the Gungan commanders in the battle of Naboo (and was even addressed as "General Jar-Jar"--something which I doubt would be given to him JUST because he had interactions with the surface-dwellers on Naboo), and was with the group for the entire movie despite being extremely clumsy. If he is competent in SOMETHING, that would explain his presence--that he's not entirely useless. Why would the group bring Jar-Jar into the city on Tatooine? He was nothing but a liability due to his clumsiness. He had to have had an in-universe reason to be brought along. Furthermore, he was among the Naboo delegates in the future movies, so he clearly had earned some respect.

Sidious had a secondary purpose for his invade-Naboo-scheme.
The primary purpose was exploiting the situation for political gain - which would work regardless of whether the Trade Federation's plan worked out or not. The secondary purpose was to act as a test to decide if he should become the absolute ruler of the Galaxy through the Confederacy (or an analogous organisation of Separatists) or the Republic. If the Trade Federation had won, Palpatine would have aimed to rule the Galaxy as The Man Behind the Curtain to the Separatist Council, Darth Sidious, rather than ruling openly as Emperor Palpatine of the Republic-derived Galactic Empire.

Qui-Gon and Maul were Working Together
In fact, they had some kind of suicide pact, hence Qui Gon's reaction to Anakin's claim that Jedi never die. Qui Gon had planned his death because both he and Maul were on the same side and were helping each other find the one to bring balance to the force; Maul just worked for Sidious as a cover. Qui Gon and Maul didn't trust Sidious; because the Prophesy was vague, they didn't want to take their chances with having Anakin around Sidious if Maul were to train him. Qui Gon also trusted Obi Wan with Anakin, but he couldn't have two apprentices. So, he decided to give up his life to have Obi Wan train him. However, he and Maul knew that if Sidious found out Maul would pay dearly for it and it would endanger their plans. Qui Gon knew that Obi Wan had an impulsive side to him that Obi Wan didn't want to admit to, so Qui Gon and Maul decided to use it to their advantage (the other reason for Qui Gon's death). Maul slaying Qui Gon would trigger Obi Wan's anger and this would bring about Maul's death. By dying, Maul would take his and Qui Gon's secrets with them.

Jar-Jar is a character suggested by studio executives.
They pressured George Lucas to add this horrid character in the movie because they think it should appeal to little kids.
 * Because if anything explains the problems with The Phantom Menace, it's George Lucas not having enough influence over the project.

The story of Anakin is a story of George Lucas himself.
Lucas wanted to write a tragedy of himself being an independent filmmaker/artist who is corrupted by the dark side (aka. money). That is why Vader is promoted from being a decorated henchman to SPACE JESUS in Lucas' grandiose writing (albeit sloppy and incoherent). Anakin/Lucas then becomes the leader of a vast empire in which he never more has to discuss stupid and evil decisions with his peers.