Yokohama Kaidashi Kikou/WMG

Humanity itself is either downloaded into a computer brain simulation or off living elsewhere in the galaxy.
Because it may feel slightly petty of me, but I don't want humanity to be going downhill. Most people on earth downloaded themselves/left for the stars, and the remaining folks decided that war, government, and all that bad stuff wasn't worth their time, so they just chill and let most of the world return to nature. Allows me to chill reading this without feeling a bit down.
 * Or they downloaded themselves into the robots. How's about that for ya?

Alpha was here long before the great flood, and Mr. Hatsuneno left before the flood as well.
Alpha wouldn't consider this to be the twilight of mankind if not for prior knowledge of what kind of life mankind has lead before this.

The human race knows that it is doomed, and the Alpha series is designed to be their final legacy.
You see fewer and fewer humans the further the series goes. Alpha is a living museum as to what humanity was, and so the next civilization, sentient race, or whatever aliens show up in the far future can have someone to learn about us from. This may be kinda obvious from the setting, but the reasoning behind the creation of the androids is never outright explained...
 * Humans (in Real Life, anyway) don't seem to need a reason to invent androids that goes much farther than, "Hey, wouldn't it be cool if we had robots that were like people?" Oh sure, we'd find uses for them, like eldercare (a big field for robotics in Japan) or dog-walking or housekeeping or killing other robots, but the driving force seems to be "because we can." More poetically, the desire to create is woven into the fabric of our race, made as we are in the image of the Creator; what creation is more grand, more complex, more wonderful than life like our own?
 * This doesn't exactly accord with the conclusion of both Ayase and Alpha that androids are the "children of humanity," which makes it sound like they will themselves be the successors.
 * Maybe those "mushroom people" will turn out to be the new successors.
 * And the robots will be along to pass on humanity's memory and legacy to them.
 * In either case, Alpha and her ilk won't have eternal life themselves, either; they are machines, so they need need parts and maintenance--which will likely be hard to come by once people have disappeared.
 * Given how staggeringly advanced the robots are, their learning to maintain themselves and reproduce hardly seems far-fetched. The robots will eventually inherit the earth, becoming self-sufficient and replacing humans, just as children eventually become independent and replace their parents. It also fits the whole childhood and transience of things themes that run through the piece.

== The human race built the Alphas, and then when the need arose, they set them to keeping the lights on while they went away and waited for the planet to sort itself out again. Some humans opt to stay behind to help maintain the infrastructure. ==
 * It's a common-enough trope in the various media: The planet is used up or becomes similarly unwelcoming, and so humanity -by far the biggest strain on Earth's systems- packs up and moves to a sort of vacation home while repairs are being made. Wall-E, most recently, but also games like Vectorman and a book I heard about once. This may be the twilight of humanity, but twilight is by definition not forever.

Yokohama Kaidashi Kikou ties into the Mega Man franchise
This requires that either there are some humans left in the world (Dr. Light and Dr. Wily), or Dr. Light and Dr. Wily themselves are robots. Either way, most of the planet is populated by normal robots, and what we see in the Mega Man series are extraordinary robots granted special powers. Thus, Yokohama Kaidashi Kikou is a Slice of Life version of Mega Man following the lives of the more normal robots.
 * Thus the lack of male robots - most of them have been captured by Dr. Wily and converted into his Robot Masters.

The world of Yokohama Kaidashi Kikou is a by-product of Instrumentality

 * This would explain the lack of humans - the only humans who are present are the ones who rejected Instrumentality. The robots are either EVAs, or Angels who rejected Instrumentality and have constructed robot forms for themselves so that they may peaceably interact and live with the humans. The robot backstory is just a cover they invented for themselves, taking advantage of Instrumentality to implant the memory into the minds of everyone (including themselves).
 * Alpha is EVA-01, her unseen "owner" is Shinji, Kokone is EVA-00, Maruko is EVA-02, Sensei is Ritsuko, Nai is Kaworu, Misago is Rei, Takahiro is Kaji, Makki is Misato, and Ojisan is Gendo. The "mushroom people" are either those who have accepted Instrumentality or those stuck somewhere in between.

The "ghost" that Ayase tells Alpha about (in Chapter 99: Surface of the Earth) is Alpha herself
Ayase mentions that there are rumors of the area (where the cafe would later reside in) being haunted. He mentions that this was during his childhood, before the cafe was opened. It's likely these rumors started after passers-by noticed how unusually tidy such an otherwise derelict little town was and surmised that a spirit must be watching the area, unaware that the area's upkeep was Alpha's handiwork.

The global disaster that forms the setting of YKK was genetics run amok
Long before the manga's setting, some scientists (or a group of scientists) set about on some breakthroughs in genetics research, principally genetic manipulation. Their motivations may have been varied: research for the sake of research, the solution to global agricultural depletion, the development of crops better suited for an environment afflicted with global warming.... Anyway, they created a plant or crop with adverse side effects. It quickly "broke out" and proliferated, disrupting the balance of the atmosphere's composition and aggravating the already serious global warming problem. It was able to cross-pollinate and hybridize with a wide variety of plant species; hence, the mushroom-like "shrines" and other people-like figures, plants imitating street lamps, and sunflowers three stories tall. Fauna became affected as well, as evidenced by the "kamas."

Misago is a genetically mutated human resulting from the described theory above (or another mutation theory)
A large portion of the populace became infected and mutated; they reverted to a feral state and essentially became immortal. They also became infertile. This was enough to cause most humans to lose faith in their own reproductive abilities; hence, the creation of Alpha and the reason the human population is declining: it's a fear-based voluntary extinction.

The "A2M1-4" records Kokone discovers and becomes obsessed about are the A2M1-4 units themselves
Nobody said the earlier "Alpha" series units had to be robots. Earlier unit runs could have been trial programming code. Programming code can be expressed in many, many different ways - yes, even audio recorded on a vinyl record. The exact nature or meaning of this coding may be lost forever; the current Alpha robots seem to be the only ones capable of comprehending the audio, and it seems to directly affect their mood. It's possible the A2M program centered around the development of cybernetic emotional skills or thought-process manipulation. It could possibly be a program used to keep Alpha series robots in check to prevent a "Matrix" or "Terminator"-style robot insurrection. (This would explain their placement early in the "Alpha" sequence; surely, you'd want to have a means to prevent a robot resurrection early on, preferably before the robots are built.) It could even be the programming for a primitive AI encoded onto a vinyl disk. The "M1-4" model numbers may indicate that four such programs were produced, meaning Kokone has located all of them; or it could refer to the number of programming "tracks" each disk contains.

Ayase is wrong: Misago is a feral robot, specifically an early Alpha prototype
In Chapter 83, "Blue Sound," Sensei talks about the first of the Alpha series robots created. Her description of the robot is overlaid on top of an image of (what is presumed to be) "Director Alpha," but it could just as easily describe Misago. It would explain everything rather conveniently, especially Misago's lack of age. (And of course Misago can survive on fish; Alpha's protein allergy is clearly limited to her). When Ayase stated that Misago predated the invention of sentient robots, he was simply wrong; he never experienced a world without them, so how can he know for sure what existed before them or how long they've been around, especially since the global devastation wiped out much of the human records?
 * In which case, Misago might be one of the two unaccounted for A7M2 units (and Alpha's direct sister) or an earlier robot (such as an A6 model?)

Misago is a Highlander
Why not? There Can Be Only One!

Misago is not immortal nor a single individual
"Misago" rather represents an entire race - let's say of genetically mutated humans, though it could be something else. This race may live underwater or on a small isolated island near shore. Every now and then, some of the girls venture far from their normal hunting grounds and try to approach humans. Children are less likely to be harmful, so the Misago naturally tend to gravitate towards them more; or perhaps the Misago themselves are children. They all look alike because of creative license; in reality, nobody ever gets a good glimpse of them, and therefore no one can tell them apart anyway.

Misago is the fully matured form of the same type of creature as the water god shrine/"mushroom people"
The "face" seen on the "water god shrine" is the larval stage. Over time, it will appear more and more human until it eventually leaves as a fully mature Misago. It's possible that this stage takes a long time to gestate. Whether a Misago can live a very long time, or if we've been seeing different Misago as per the above theory, is left open.

The "mushroom people" are Hatsuseno-sensei's creation, and Misago is a prototype
In chapter 21, When Ayase sees the face of the "water god", it immediately reminds him of Misago; afterwards, he's seen thinking of Hatsuseno-sensei and wondering what he may be up to. What he is "up to" is sowing mushroom people around the country: the creatures are his creation, and Misago is a prototype left behind.

The "Alpha" series of "robots" are not robots at all, but the fully matured form of the same type of creature as the water god shrine/"mushroom people"
The only evidence we've seen that they're "robots" is, they can plug things into their mouths and the humans around them keep insisting they are. (Even a wetware human could plug something into her mouth if she had an outlet for the plug there; it just so happens to be that the tongue, with its direct connection to the brain and large concentration of nerves [taste buds], is a convenient place to put one.) Perhaps the "water god shrine" is the result of some genetics experiment related to the next evolution of humanity; when they fully mature, they are "harvested" and educated, brought up to believe that they're robots. Perhaps the humans believe this will be less of a shock to them than believing that they're weird genetic mutants; just as likely, the humans in on this figure that the locals will accept cute robots but go after mutants with torches and pitchforks. Kokone can't uncover any records of "Alpha" series robots because they never existed. The Misago are Alphas that escaped and went feral before they could be "harvested."
 * The reason males are so rare is that this particular plant/animal hybrid has a much lower probability of producing a male than a female.
 * There's other evidence of robot-hood: Sensei's repairing Alpha with plastic sheets and artificial hair.
 * Do we know that for sure? It could all be part of The Masquerade in the form of simple plastic skin grafts and such. Even humans in Real Life can take a few plastic parts.
 * Alternatively, they are cybernetically enhanced artificial humans or the result of experiments where a computer brain is put inside an organic body grown in vats.

The "Alpha" robots are directly responsible for humanity's post-apocalyptic decline because they compete with human females
It's like the episode of Futurama in which Fry tries to date the Lucy Liubot and the Professor shows him the educational video about dating robots. In the manga, most of Kokone's male co-workers are competing for her attention (though Kokone is oblivious to this until one of her female friends points this out to her very late in the manga), and the vast majority of Alpha's customers (who are overwhelmingly male if we only count each customer once) brave the broken trails to Alpha Cafe just to meet her, knowing full well that there's little chance of anything palatable once they get there. In fact, Alpha herself seems to be a major reason the town's still on the map. Perhaps female robots were so successful in competing for human males that the human population began dying out; nobody wanted to bother with fleshbag females anymore. This might reveal a more sinister motive behind their creation, and the reason there are so few male robots: there was a greater demand for female intelligent walking sex dolls than there was for male ones.
 * But there aren't enough female robots to go round, and if a man can't get exactly what he wants, he'll settle for second best... We're not particularly picky animals when it comes to what he have sex with.
 * Gee. Thank you. Thank you very much for that pleasant mental imagery.

Alpha was Dead All Along
Exactly What It Says On the Tin: Alpha is was a human who was a casualty of World War III (possibly a nuclear strike) and is either in heaven or in a state of self-induced limbo built upon a Yokohama ravaged by nuclear warfare. (Hence the rising seas and deserted towns.) The humans are all those she has known who have died; the robots are new friends to keep her company for eternity - after all, robots don't die. Misago possibly represents her Id, Maruko represents her ego, and Kokone represents her Superego.

Alpha is really Sensei, and the whole thing is a simulation
Sensei is running a compressed lifetime's worth of simulations in her ongoing AI research from the perspective of an AI interacting with true AI programs (which can range up to absolutely everybody else), simultaneously determining how AI will react differently if it knows it's a robot as opposed to thinking it's human, and how the AIs will react under varying degrees of isolation. There are few robot males because Sensei is testing what would happen with that parameter. There is no explanation for the decline of humanity because it's not needed; just program the parameters and go.
 * Alternatively, Alpha, Kokone, Maruko, Director Alpha and Nai (and Misago, if you believe she's a robot) are all in a gigantic Truman Show Plot setup where they're intentionally kept in an isolated environment with limited contact with humans and with little to clue them in on the history of their environment to study how well robots will react and integrate into society. They're all prototypes testing different personality aspects. Misago's testing wilderness survival skills.

The Alpha robots are so human-like because each one is built around a Spark
Sensei was able to achieve a breakthrough in cybernetics, not through her own research, but because she stumbled upon the deactivated corpse of Megatron. While she was fiddling around with him, the rest of the Decepticons discovered his location and attempted to rescue him, razing Yokohama in the process. The Autobots came to the rescue, but too late; as compensation, they allowed the humans to copy Autobot sparks to create robots that would help and provide companionship to the remaining humans of Yokohama.
 * Alternatively, they were granted life through the All Spark.

The weird "mushroom people," "mushroom buildings" and "streetlight trees" are all living manifestations of The Force
Perhaps the genetic experiments proposed in one of the theories above was related to midichlorian research - perhaps it was even responsible for creating midiclorians. A lab accident resulted in these midiclorians breaking out; like their real-life counterparts, mitochondrians, they quickly spread and entered into the cellular structures of the local flora. It's even possible that, in large enough concentrations, these midiclorians even created life forms of their own. These new Force-sensitive beings were then imprinted with the memories of all those around them, especially the local human population.
 * Misago is a Force-sensitive being, perhaps even on the same level as a Jedi Master; this is what grants her immortality and the ability to hide from other people.
 * Misago may be tapping into Sith powers - she had discovered the secret to immortality that Darth Plagueis, Darth Sidious/Emperor Palpatine and Anakin/Darth Vader had been searching for.

Along those lines, the "Alpha" series of robots became sentient through the Force and are therefore Force-sensitive.
Makes sense if they're fully matured "mushroom" beings like one of the above theories states; but even if they are robots after all, Obi-Wan and Yoda did say that the Force is in everything. Who says that robots can't be Force-sensitive?
 * The transfer cables the robots use to transfer memories between each other and other machines are functionally useless. In reality, they're tapping into their Force powers to experience whatever they wish to extract from their targets. Either they just haven't caught on yet, or the humans have caught on and invented the "transfer cable" hoax to prevent any of the robots from discovering the full extent of their Force powers and potentially turning Sith.
 * Too late in Misago's case. Hope the humans have lots of ysalamir with them if she ever decides to turn to the Dark Side.
 * Alpha's dreams are a result of the Force trying to speak to her.
 * Alpha meeting Kokone, and Maruko meeting those two, are no accident; the Force directed all three towards each other. Together, they'll form their own Jedi Council to rebuild humanity and society.
 * The Director robot knows about the Force, attained Jedi Master status (or maybe even Jedi Grand Master status), and is using that power to look after the rest of the world as best she can.
 * This theory might have some basis. As it turns out, there were robots in Star Wars who were actual Jedi Knights; these were appropriately called the Iron Knights. Iron Knights were in fact droid bodies for Shards, Force-sensitive crystalline creatures. Shards were known for being extraordinarily patient, long-lived, extremely curious about other living things and the world around them, and able to interact with computer technology - sound familiar? Perhaps whatever resulted in the formation of all the other "weird" stuff in the world also formed Shards, which were then discovered and put into robot bodies. If these were the result of Midiclorian research, then Alpha and the other robots may eventually become "Iron Knights." The Director robot likely already discovered this, as discussed above.
 * Don't forget Skippy the Jedi Droid who may or may not have been a Force-sensitive droid who may or may not have had a Shard. Yes, Skippy, the Jedi droid.

The "present" Alpha's owner wanted to give to her was not the camera, but Kokone
Alpha's owner probably figured out that Alpha would get very lonely after a while, especially since her cafe sees very little actual business. Furthermore, he probably knew Alpha had never met a robot before. In a weird and pacifist Xanatos Gambit twist, her owner arranged for a courier service to deliver a flimsy excuse camera using another Alpha-series robot with the full intention that they meet and become friends, (among other things). To ensure that they send an Alpha-series robot and not a human, Alpha's owner also instructed the courier service to deliver the message Kokone transferred to Alpha; this would also teach Alpha how to interface with other robots. Truly, a gambit Light Yagami, Char, and even Xanatos himself would be proud of.
 * Makes perfect sense, since he could bring a camera by himself (remember a note he left for Alpha in the first chapter) or send a letter with a camera. But still, the camera isn't just an excuse; it has its own important purpose.

The nature of the relationship between Alpha and Kokone is....

 * Perfectly innocent. Seriously, stop reading so much into it, you perverts!
 * Full-blown lesbian in nature. Male robots are rare, so what choice do they have? Plus, at the very end, Kokone moves in with Alpha; they presumably live the rest of their lives together. Maybe Kokone just got tired of making all those long trips, but then again.... Also, they kiss in order to share experiences with each other. What more evidence do you need?
 * Alpha's owner wanted Alpha to engage in a lesbian sexual relationship. Maybe because he knew full well that males were too rare, or maybe that's how he honestly gets his jollies worked up.
 * Why should robots have sexual orientation? That's a qualification for human behavior. We're talking about robots, which have no gender by definition and thus don't need a sexual orientation, despite what they might look like. They are simply intelligent beings that somehow have a human-like longing for close emotional (and physical) connections. One wonders why the makers would make robots that can experience such emotional turmoil when it would have sufficed to simply let them mimic feelings. We wouldn't have much of a story if that was the case, though.

Kokone is a well-tempered, patient Psycho Lesbian (and so is Maruko)
Or, to put it another way, they're both lesbian Yanderes. Think about it: Kokone seems outright obsessed with Alpha, visiting the cafe as often as she can, always talking about Alpha, and eventually moving in with her. It seems a bit clingy. And, ironically enough, Kokone has a stalker of her own, Maruko. Maruko seems just about as crazy for Kokone as Kokone seems crazy for Alpha; this is perhaps most visibly illustrated when Maruko practically ambushes Kokone, causing Kokone to pull out her gun on Maruko. Yes, Kokone probably pulled out her gun in fear that she was really being ambushed, not knowing it was Maruko, rather than being genuinely afraid that Maruko was finally enacting a dangerous stalker fantasy, but c'mon, what kind of normal person or robot would sneak up on somebody like that?!
 * This also affects the relationship between Maruko and Alpha. Maruko is suspicious and distrustful of Alpha because she's competing with her for Kokone. Every time Maruko comes to Alpha, it's always to "check the other side out," which is why she's nowhere near as open to Alpha as Kokone is.
 * Maruko's jealousy was further inflamed when she saw Alpha made friends with Nai, who had a past relationship with Maruko.

At the beginning of the series (and possibly throughout), Alpha was bipolar (manic-depressive) or suicidal
After possibly many years of being lonely, and with little to no business coming in, Alpha entered into a state of severe manic-depression or bipolarity and contemplated suicide. The scenes near the beginning of the manga's run, in which Alpha is beside herself with a gun on her desk, represent Alpha's contemplation of suicide. Her meeting with Kokone and their friendship "cure" her of this, but she still shows many manic-depressive or bipolar signs in her behavior and interactions with other people. She even contemplates suicide again when she starts shooting a signpost with her gun; she had originally decided to take her own life, but she had a last-minute change of heart and had to justify to herself taking a gun out back with her being alone.
 * Shortly after the manga, after Ojisan and Sensei pass away, Kokone is killed in an accident; upon discovering this, Alpha finally does commit suicide. The image of Kokone's busted, offline corpse before she pulls the trigger is the "last thing reflected in Alpha's eyes" that Ashinano Hitoshi asks the reader to imagine. This was in fact the original ending to the manga, but Ashinano thought it was too much of a Downer Ending; so he changed it, but couldn't think of a definitive end, so he left it open. The "epilogue" chapter was going to build on this ending with Saetta finding the two robot corpses in the cafe shop, but that was likewise moved "off-screen."
 * Or how about this: Kokone suffers an injury which immobilizes her, but this occurred after Sensei, the only person qualified to repair Alpha-sereis robots, passed away. Seeing Kokone in such pain and depression, Alpha decides to commit a murder-suicide (or assisted suicide-suicide, depending on how you look at it). Thus, the "last thing reflected in Alpha's eyes" is the image of a gunsight aimed at Kokone's head. Of course, in addition to being ridiculously depressing, this is beginning to head more into Fanfic territory than actual WMG territory.
 * Those territories have considerable overlap.
 * Alpha was not saved by Kokone; she did commit suicide at the beginning of the manga. Everything that happens after that is all just a happy illusion created when she entered Robot Heaven.
 * Alpha's owner gave her the gun specifically to commit suicide with if things got too lonely and unbearable or if Alpha became too injured to carry herself to a doctor (or if all the remaining qualified doctors died out). This is similar to a practice during WWII where American pilots assigned to missions over Japan were issued handguns, not to defend themselves with, but as backups in case their cyanide pills failed (which often happened).
 * Before anybody says the guns just have electromagnetic "stun" bullets, we don't know what type of bullets Alpha had loaded in the gun when it was on her desk. Also, it's possible there are different type of electromagnetic bullets, including ones that are designed to outright kill robots. These may be the type Alpha was shooting at the sign with.
 * Or maybe shooting herself with stun bullets is the robot equivalent of wrist-cutting.

Ashinano Hitoshi pulled a Hideki Anno and Yokohama Kaidashi Kikou is ultimately the product of bipolarism or depression
Relates to the above theory: ultimately, Yokohama Kaidashi Kikou is about Alpha finding meaning in her existence. Alpha is an Author Avatar for Ashinano. The whole work is an allegory for Ashinano's own struggle to find meaning and purpose in his own life.
 * Yokohama Kaidashi Kikou is just yet another Neon Genesis Evangelion rip-off without EVAs, Angels, NERV, SEELE...or anything else, for that matter. Just like the Bible.

Maruko is a transgendered robot
"Maruko" is actually a male name, as Kokone and Maruko herself point out. And she does act and look very tomboyish....

Maruko was once a slave
This is why she refuses to take on the family name of her former owners and why she insists on being so "independent."
 * Tie-in to the above theory: Maruko was once specifically a sex slave, and this influenced her later behavior. This is why she adopted a male name, a tomboyish attitude, and an unusual, arguably creepy relationship with another female robot. She wishes to become a male, and probably would be if sex reassignment specialists for robots were more commonplace.

The reason there are so few male robots is that most robots chose to be female
Robots are allowed to choose their own gender; most of them, for whatever reason, just prefer being female.

A key figure in the past of YKK is Grant Imahara.
The WMG page for Myth Busters states that Grant will be an activist for "robosexual rights." Hmmmm....
 * Alternatively, Grant time-traveled back from the future of YKK and wants to set things right before the Cosy Catastrophe happens...and champion robosexual rights while he's at it.

The reason Alpha and Kokone have handguns for self-protection is that they need the self-protection
Past experience, whether through their own experience or from lessons learned through the interactions of older robot models, have probably told Alpha and Kokone that female robots are frequent targets of rapists and stalkers (which is odd, because most science fiction tells us humanoid robots will automatically have the strength of ten men regardless of the robot's sex or gender). Hence Kokone's reaction when Maruko "ambushes" her.
 * Makes sense from a marketing perspective to have weak androids; of you make them as frail and fragile as a standard human, people would be less likely to be intimidated by them and more likely to purchase them.
 * Alpha's owner gave her the handgun specifically for this, even though she doesn't know why. She understands the concept of "self-protection," but the concepts of "rapists" and "stalkers" are foreign to her; this is why the clingy attitude Kokone has with her doesn't faze her one bit.
 * There may be roving gangs of "robot slavers" who capture and enslave robots, similar to such Real Life gangs as plague Thailand, Eastern Europe, and hundreds of poorer countries. Playing with some of the above stated theories, Maruko may be an escapee of one such gang.
 * Alternatively, like the above suicide theory states, robots are given guns by their owners specifically so they can commit suicide if they're too injured to carry themselves to a doctor, all the doctors have died out, or if they simply become too depressed from isolation.
 * It could also be that it is usually problematic to let robots live together, since they tend to be very aggressive in their search for partners who won't die long before they do. Robots are thus sometimes given guns to defend themselves against other robots.

Alpha is Yotsuba
. See that WMG on the Yotsuba&! page for more details (though it ain't much, and maybe just as well).
 * Copied from the Yotsuba&! entry: "I have seen a report of paired cross-over fics (or possibly doujinshi, it was unclear) called "Alphato!" and "Yotsuba no Kaidashi Kikou" about, respectively, a man who becomes the owner of a green-haired android, to help socialize her in a suburban neighborhood, and an energetic orphan adopted by the proprietor of a lonely country cafÃ©, and the havoc she wrecks among the neighbors. Needless to say I WANT THESE NOW."
 * Or maybe that should be reversed: Yotsuba grows up to become Alpha.

Yokohama Kaidashi Kikou and Courage the Cowardly Dog take place in the same universe
Courage The Cowardly Dog is about how the people of Middle of Nowhere, Kansas (all two of them) cope with life after the same global disaster shown in YKK. The world of CtCD has shown us that they do possess a highly advanced understanding of robotics - a random Chinese tourist was able to build a "better robot dog" that showed a high degree of advancement. The weird events and creatures that happen to Muriel and Eustis are manifestations of the same phenomenon that created all the "weird stuff" in Yokohama - only, instead of imitating the shapes of buildings, people and lamp poles, they try to kill everything. They do say After the End tends to be harsher and more "Badass" in the U.S. than other parts of the world.

Aperture Science is responsible for developing the "Alpha" robot series; "A1M1" is GLaDOS
GLaDOS was abandoned in the Aperture Science Enrichment Center when she began to develop a personality and the ability to express emotions (and began to turn psycho). The guys over at Aperture started poring over any information they could find to figure out what went wrong; one of them did, figured out how to replicate the coding that gave GLaDOS a personality, and modified it so that it wouldn't be so prone to lapse into psychotic episodes. They then sold this technology in order to recoup their losses from the portal gun project, which had been left abandoned in the Enrichment Center (if it was not smuggled out).

The global disaster in YKK is, in fact, the "Seven Hour War" and the Combine invasion.
The human population is slowly disappearing because it's being harvested by the Overwatch. A reproductive repression field also blankets Yokohama, but nobody's aware of it. The Overwatch consider Yokohama to be too sparsely populated to post soldiers there; but, had Alpha continued her journey to the most populated parts of Japan, she may very well have run into Metrocops. The Director robot and the Tarpon spend so much time over the skies of Yokohama because the Combine's presence is the least visible there and, therefore, she has the least chance of being intercepted and shot down.
 * Kamas, the "mushroom people," the "streetlight plants" and three-story sunflower seed are either synths or the results of crossbreeding with synths.
 * The "mushroom people" represent the larva stage of synths, quite possibly adviser synths. The Combine choose Yokohama because of the limited human presence, their lack of understanding and exposure to the Combine, and their highly mystically-rooted beliefs (that is, the villagers are more likely to believe that they're "water gods" and the result of "implanted memories" than alien creatures being raised to maintain the Combine occupation).
 * Kamas are highly mutated headcrabs, or vice-versa. Alternatively, they're a larva stage of dropship synths.
 * Most male "Alpha" series robots were destroyed as a result of the "Seven Hour War."
 * The Combine have established an Overwatch over Yokohama; it just never shown. Alpha and Kokone have guns so that they can defend themselves against Metrocop or Overwatch harassers, or from headcrabs and antlions.
 * Alpha will eventually meet Chell and Gordon Freeman.
 * Alpha will amaze Kokone and Maruko when she starts thinking with Portals!

Yokohama Kaidashi Kikou takes place during or after the Eugenics Wars/WWIII
Japan was caught in the crossfire between Khan and his foes, resulting in the destruction and rising sea level seen in the manga. The "Alpha" series of robots were developed in reply to Khan's eugenically modified forces. Humanity does eventually recover though, for some reason, the technology behind the "Alpha" series is lost...until one day, when Arik Soong digs through some ancient records and finds some old, mysteriously labeled vinyl disks, and wills them off to his grandson Noonien....
 * The "weird mushroom stuff" and other strange flora phenomenon are the results of Japan trying to duplicate their own Augment program; this program was considered a failure and abandoned in favor of the "Alpha" series.
 * Consider what we know of Alpha and her sisters and brother, and what we know of Data from Star Trek the Next Generation. In TNG's Season 1 episode "Datalore" (which introduces his brother Lore), it is revealed that Data's structure utilizes at least some biological components (something Data himself confirms in "Deja Q" which also revealed his need to eat in a fashion very similar to the A7 androids), something long suspected by many to also be a trait of A7 androids. Also in that same episode (as well as another season 1 episode, "The Naked Now"), Data can also be drugged with effects similar to humans; the A7 robots can be drugged as well, resulting in the temporary elimination of inhibition similar to that seen in humans (alcoholic consumption makes Alpha lose her shyness about dancing in front of others). Both Alpha and Data have fallen from similar heights without bodily injury. Finally, in the Season 6 episode "Birthright," Data began experiencing dreams similar to Alpha's.
 * This would also explain why Hikaru Sulu is so fond of dangerous plants.

Humanity bounces back in the end
It seems as if there's a general consensus that humanity eventually dies off in the end even though there's not a lot of evidence corroborating this. Director Alpha notes that the populations are shrinking, and humans factor less and less as the series goes on, but humans are still present throughout the series to the very end. In the last few chapters, Kokone visits what appears to be a rather busy (if not outright bustling) city, and the very last character to appear in the series is a female human - one who hadn't seen birth until nearly the very end of the series, no less.

A major theme of YKK is unrequited love
All the credit needs to go to a poster at Yokohama Kaidashi Kikou @ pander.us. Said poster pointed out that Alpha seemed to be most attracted to Ayase, who only encountered her twice. Alpha was also highly interested in Nai, but she didn't even leave Kokone a note when she left wandering about. Therefore, the relationship between Kokone and Alpha might be entirely one-sided. In the meantime, Maruko's relationship with Kokone is blocked by Alpha. Sensei and Ojisan, despite having spent their youths together, admit that they've spent their lives alone.

Yokohama Kaidashi Kikou is a pre-history of Battlestar Galactica (2003 specifically)
Doesn't take much of an imagination to imagine that most of the human population have gone off-world to establish new colonies, leaving Earth in the hands of the Alphas and their descendants, the Cylons.

Alpha is a robotic trust fund baby, or her Owner is her sugar daddy
Another theory from Yokohama Kaidashi Kikou @ pander.us. For someone who makes little to no money (she's never once seen even handling money), she sure seems to get by. Nobody has caught on because her Owner instructed her to be discreet with their fortune.
 * Maybe Japan went communist?
 * Alternatively, it could just be that everything's on a barter system now, given the small farming community nature of everything.

The "Alpha" robots are destined to die off soon after humanity
Yet another theory brought up at Yokohama Kaidashi Kikou @ pander.us, though really this should be evident to anyone putting enough thought into it. Even if their bodies are able to remain functional for thousands of years otherwise, they're still dependent on a fuel source. The question of whether there are enough robots around to maintain a sufficient infrastructure to keep themselves fueled is not answered even though robots seem rare enough such that meeting more than one or two is a seldom occurrence.
 * Perhaps, far enough into the future, surviving robots will be forced to go feral. Imagine Misago being joined by two other mysterious figures through the shadowy mist, looking on upon the ghostly remains of a quiet little coffee shop, something deep within their buried memories telling of a long-forgotten connection.

Planetarian is a prequel to Yokohama Kaidashi Kikou
Both take place After the End, both feature Ridiculously-Human Robots that are female, the main characters of both series are learning to cope with loneliness as they wait for their owners, and both main characters develop attachments for those few humans who stick around. Given the circumstances of these works, Planetarian should fit almost seamlessly into the same timeline as Yokohama Kaidashi Kikou, during the final stages of the war that led to humanity's downfall. The Planetarian robot would be an early Alpha-type robot, maybe the same one buried under the grave Kokone ran into before she entered the library.

Most of the humans left Earth for Mars/stars/whatever
The Earth was considered no longer viable, and so they left behind whatever humans wished to stay and some robots to look over the Earth and perhaps one day restore it to its former glory. Hmmmm, kinda sounds familiar....
 * The basic setting of YKK is a kind of a cross between The City and the Stars and With Friends Like These... -- humanity became so advanced that it got bored with simply living on the same old Earth and just went... somewhere, leaving behind those not wanting to emigrate. Robots were made because the remaining population was too small to sustain itself and the technology. This tech is truly breathtaking: the robots are obviously made from scratch, but they are absolutely indistinguishable from humans except for a couple of specifically added traits. And then there is Taapon, which is simply impossible unless they know some material couple of orders of magnitudes stronger than current materials science is able to predict. So there weren't any cataclysms -- just abandonment.

The "water gods"/"mushroom people" are the graves of deceased robots
Yet another theory proposed at Yokohama Kaidashi Kikou @ pander.us. If the robots have any significant organic components in their construction (such as a fungus-like substance), this organic substance can continue to grow and thrive long after the robot itself had died, taking on the shape of its previous form.

Alpha and Nai did it
Alpha seemed shyly excited about Nai's, ummm, manhood, and they did spend the night together. We do know that robots can transfer memories by tongue-on-tongue kissing, so it's possible there's memory/sensory transfer during full-blown sexual intercourse. Wouldn't it be ironic if Kokone transferred Alpha's memories to Maruko after they had been transferred from Nai to Alpha during a night of hot steamy robot love-making, rather than Nai's memories directly? (Nai and Kokone had to have had met in order to get the memories in the first place; who knows, maybe Alpha was still there too, and Kokone wouldn't have resisted a quickie from the object of her desire).

Kokone and Nai did it
Why not? If Kokone and Nai met, well...maybe robots have a very loose concept of sexual morality, and maybe only Maruko is the jealous type.
 * Not like they can get pregnant or STDs, after all.

Kokone and Maruko did it (and routinely do it)
C'mon, this one's practically Word of God!

I call Poison Oak Epileptic Trees on all WMGs involving Gratuitous Promiscuous Robot Sex.
Mainly because the humans appear to have made them as human-like as possible; if this didn't include something as basic as sexual mores, there'd be little point.
 * If they didn't include something as basic as sexual mores, that would be the whole point of them being as human-like as possible.
 * And as above, humans often get more promiscuous (though not arbitrarily so) under conditions of total safety.

YKK doesn't take place in Yokohama, but on an alien world, and the "robots" are plants
. The world or humanity isn't diminishing, but rather rebuilding, and everything is in a state of reconstruction rather than decay; plants (Trigun terminology for advanced sentient aliens able to manipulate the laws of physics to their will) are trying to turn the planet Gunsmoke (think Tatooine) into a copy of old Earth. The mushroom buildings and streetlight trees are the visible parts of this process. As for the robots, they themselves are plants who have decided to take human form and intermingle with the humans much as Vash and Knives did; they have either forgotten about their powers or have intentionally kept them hidden.
 * If they've forgotten their powers, one hopes Maruko doesn't rediscover them, get jealous at Alpha, and turn Knives on them!

== All the deep meaning and symbolism Ashinano Hitoshi created for Yokohama Kaidashi Kikou is all just accidental and manufactured ==. According to this site, Yokohama Kaidashi Kikou has a "huge following...in Japan among exhausted salarymen on their way home after a week of 12 hour workdays." Now let's take a look and examine that for a little bit. The stereotypical portrayals in works such as Crayon Shin-Chan and other anime and manga works will do for a starting point. Now, what kind of picture is an exhausted salaryman going to idealize after 12-hour workdays, especially in Japan? Well, first of all, he's probably going to idealize a setting with the absence of monotonous work, probably a setting rich in pretty pasture lands and other rural imagery. Large cities would be banished from this picture because they represent the overcrowded conditions the poor salaryman has to put up with on a daily basis. Now, what else is this tired worker going to idealize, especially when he gets home? A faithful, beautiful woman with a lust for life, (among other things), who nonetheless exerts a healthy independent attitude. (In other words, the exact opposite of Mitzy from Shin-Chan.) Transplant said salaryman's loneliness, urban claustrophobia, and longing to explore unseen lands onto the female character to create an empathetic connection between character and reader, a lesbian element for good measure, and some random elements of mystery with no intended explanation to create a "hook," and you have a surprisingly formulaic, calculated outlook on Yokohama Kaidashi Kikou.
 * Of course, with that said, it does rather sound like a genus of Poison Oak Epileptic Trees.
 * The same applies to a lot of other anime and manga series, especially the Slice of Life variety. They are basically ways to escape the rather harsh and dull reality of the average Japanese working/school life. Knowing this helps in understanding where a lot of the tropes come from.
 * Of course a problem with this that to be formulaic their has to be a formula a work is clearly adhering too. While yes in a very board sense YKK is "slice of life" in the sense of following the life of a person in which not much really spectacular happens it has very little else of what we normally associate with that term as a genre. It just clearly has a very different vibe and feel to it then the normally very happy go lucky works we tend to call "slice of life". One incident might be a coincidence, but two is a patten and the more they pile up the harder it is to ignore them.
 * There is a name for works like this: Iyashikei. They are not only a means to escape reality, but also a means to instill a peaceful feeling with the audience. For examples of other Iyashikei series see Aria and Tamayura.

In another part of the world, far away from Yokohama, Blade Runner is happening
Yes, yet another Yokohama Kaidashi Kikou @ pander.us transplant theory, basically saying that Blade Runner and Yokohama Kaidashki Kikou are happening in the same universe/timeline concurrently. Yes, that's right, Alpha and the other robots are Replicants, or at least the Japanese version.

In terms of appearance, Alpha (either of them) is a clone of Sensei's younger self (minus the green hair in Miss Hatsuseno's case)
They look an awful lot like each other. And green hair dye can't be that hard to find.

The "Alpha" series of robots are Terminators that have lost their memories
For whatever reason, they lost their connection to Skynet and forgot who they were, maybe as a result of the war. Therefore, Skynet itself is inadvertently responsible for their lost connection. The local humans aren't aware of Skynet, and so they assume they're just friendly robots. Most of the males, however, retained their connection and are off trying to kill John Connor, going back in time, or both.

Yokohama Kaidashi Kikou is an alternate result of humanity's loss against the Anti-Spirals
Lord Genome doesn't exist in this alternate outcome or is killed during the war. The humans return to Earth and set work on the Alpha series of androids, who would continue on the legacy of humanity; they would lack spiral energy so as to not incur the wrath of the Anti-Spirals.
 * But Alpha, and perhaps some of the other robots, do have Spiral energy and are powered by Spiral Energy, but are ignorant of that fact. Perhaps one day, they'll discover the truth and kick logic to the curb and drill through the heavens! (sorry, couldn't resist)

Fallout and YKK are the same universe.
No, seriously!

The cause of the rising sea levels is global warming; oil has nearly run out, hence the lack of cars and most modern technology; and all the weird creatures are mutants spawned by radiation and genetic experiments (just more... cuddly then what showed up elsewhere). The A7 series of robots were designed to endure the war and help humans rebuild after it by living long and thus retaining knowledge from before. The US did much the same thing except, instead of making cute robot women, they went with a central robot brain that controlled drones, which proceeded to go homicidal after the endâ€¦ oops. Likewise, instead of building vaults like the US, the Japanese opted to produce nuclear powered flying machines to carry key people through the nuclear war and winter.

Sadly, much like the US, this proved largely for naught, as most of these preparations failed and much knowledge was lost; luckily for Japan, though, it wasn't nearly as big a target as the US, and so some areas escaped largely unharmed (like, say, certain small out-of-the-way peninsulas). Also luckily for Japan, it didn't have more guns then people, and the slightly less harsh conditions fostered unity instead of a battle for survival, explaining its comparatively better state. Unfortunately, the residual radiation has still rendered most people infertile, and the population is slowly dying off all the same.
 * War. War never changes...unless it's Japan. Then we get cute anime girls instead.
 * Maybe they found G.E.C.K and used it fix Japan. Serie takes place in far future when society has stabilised, instead of being barren wasteland of California or Capital Wasteland.

The YKK world has moved on.
All throughout the story, we get visions of slow decay, of civilisation and genetics starting to run wild, humanity in its twilight, and the traditional concepts of time and space growing fluid as the linearity of time breaks down and turns into a kind of timelessness. The surviving people look back on the past with a nostalgic feeling. Robots, some still faithful to their human masters, are all that remain of the splendid civilisations that came before. All of this points clearly to the fact that "the world has moved on".

YKK shows everyday life in the aftermath of the Singularity.
I don't know how else to reconcile the preposterously advanced technology that produced Alpha and the other robots, while people are still relying on piston-engine airplanes, other than that the acceleration of technological change until civilization is transformed into something unknowable has already happened, everyone went off to wherever civiizations go when that happens, and everything afterwards is just the people who were in the bathroom, or not online, or just scratched their heads and said "I don't get it," at some critical moment, and stuff left lying around by accident.
 * Yeah, Fuzzy Singularity seems a decent explanation if one wants something sort of hard SF. Underwater town has lights on? Not only is someone providing power, but the lights probably had to be waterproofed to still function. Someone went to a fair bit of work, presumably as an art project. Post Scarcity, extreme surplus wealth, etc. Rogue art projects could explain all biological weirdness too. Alpha's in a backwater; somewhere else are robot cities full of designers taking digital drugs.

Scooters are vibrators
Looky

Simplest explanation is best
In the real world, birth rates in most developed countries are already below replacement, and Japan may already be shrinking in population. In YKK, this continues, with ecological collapse being helpful but unnecessary. The possibility of creating human-equivalent robots also helps: given a choice of creating a mortal human child or an ageless and indefinitely repairable robot, most people choose not to have kids doomed to die. Robots are replacing humans, though not necessarily in the same numbers, or in the same places; never fear, the factories and civilization are being maintained somewhere. Yokohama (not to mention Alpha's location) is deliberately a soft decay zone; elsewhere you have higher concentrations of robots and people, not to mention cell phones/Internet. All the biological weirdness is deliberate artistic engineering.

I can't explain the never-landing plane, though. Eccentric with nuclear powered plane? Feels more arbitrary than making people-mushrooms.
 * Solar powered ship?
 * There already is a plane which can fly without fuel. Google "24 hour solar powered plane". It's not at all unlikely we can build larger planes which can actually carry considerate amounts of excess weight in the near future. The people that designed and patented the robots would be richer than Bill Gates, and have plenty of money for relatively useless projects like building such a plane. Releasing face mushrooms into the wild to mix with the global ecosystem is a far less likely thing in my opinion, because the negative effects could be much worse, and it just affects everyone without helping anyone. Your theory also doesn't explain the small amount of robots - there would be at least one robot per human family, or a higher number of human children if so few can pay for robots.