Haruhi Suzumiya/WMG/Yuki Nagato

Originally, it was Nagato who was the "back-up" while Asakura was the original Agent assigned to observe Haruhi.
Hence her having the emotions and actually in a position to observe Haruhi, while Nagato was in stand-by in the Book Club Room. But Haruhi, being Haruhi, chose Nagato. The Integrated Data Entity switched Nagato's and Asakura's roles, something Asakura and her Sponsor didn't accept.

Nagato must obey Kyon's every command
In the episode with the missing computer club guy, Nagato freezes halfway through pointing at something when Kyon says "Hold it." I cannot remember if it is the case in the anime but in the book it is explicitly stated that she stays perfectly still despite the oncoming giant insect until Kyon says "you can move again." If you combine this with the fact that only Kyon's orders could make her open the door in the island mystery one I think this conclusion seems fairly reasonable.
 * But why? Because Kyon has subconsciously chosen her as his follower, the way the Espers are divided between Haruhi and Sasaki. This is also why she was able to hijack Haruhi's power, a feat noone else in the Integrated Data Entity can do. Kyon is also subconsciously preventing them from wondering how she did that.
 * It's like that in the anime, too, although if you're not paying attention, you can easily miss it completely.
 * More evidence for this theory in the Rampage of Haruhi Suzumiya which is what the episode with the computer game is based on Nagato must wait for Kyon's permission to alter the game, she even says "The one who placed a limit on my data manipulation abilities is you." Why does Kyon have the power to limit her abilities? She also waits for Kyon's permission before joining the Computer Club.
 * More "Yuki is Kyon's follower" examples. After the Cave Cricket incident, Kyon muses that Yuki had set it up so that Haruhi wouldn't be bored. There's a major flaw in this reasoning. At the time, not only was Haruhi in a good mood, but it was Kyon who was bored. Also, Haruhi quickly lost interest in the case of the missing Computer Club president, leaving Kyon to see the "case" through. If Yuki had come up with the scenario, it was for Kyon; not Haruhi.
 * Countered, from SOS-dan: Nagato's actions are always subtle, and Someday in the Rain shows the slight variance in her responses to different people. For example, in 16:00, Nagato indicated to Tsuruya where Mikuru was, but in 17:45, Nagato did not tell Kyon where Haruhi was.
 * There is a difference between asking a question, and telling someone to tell them something.
 * Of course, it could be just that Yuki is in love with Kyon. This is hinted with the Closed Space incident, where she messages Kyon that "Another trip to the library would be...". Kyon getting her a library card could have been the most romantic gesture she could think of.
 * And she does say "I personally want you to return."
 * Arguably, her growing feelings for Kyon are what drive her off the deep end (for a Data Entity Interface, anyway) and rewriting the universe with herself a "normal" schoolgirl and Haruhi and Koizumi no longer students at North High. Of course, this makes the escape program an example of I Want My Beloved to Be Happy.
 * Going along with the above, you could interpret what Nagato did as her wanting to spend time with Kyon, who isn't around for most of the episode. Think about it: when Tsuruya barged in and asked where Mikuru was, she immediately pointed out her general direction. What does she do when Kyon finally comes back and asks her where the rest of the SOS-dan are? She simply stares at him, then nods.
 * When Yuki uses strangely off-topic responses like "Axiomatic set theory" she is not answering Kyon's questions, without lying to him. This is her version of "classified information". She is warning Kyon off and he usually gets the hint.

Alter-Ryoko was Yuki's subconscious desire to stay human.
No form of Yuki would want to hurt Kyon, but the fact that Alter-Ryoko knew Kyon was trying to change things back when even Human Yuki didn't suggests she was created differently from everyone else in the Alternate Universe. Some small part in the back of Yuki's mind gave herself a companion in the new world that would defend it. Add a dallop of guilt for original Ryoko's erasure, mix in Ryoko's normal psychopathy, and stir.
 * Alternate Interpretation: Alternate!Ryoko is a Psycho Lesbian Stalker With a Crush on Alternate!Yuki. Why else, in the parallel continuity that Yuki had just created, was she hanging around the school at 4 am? Watching Yuki? With a knife?!
 * Why was Ryoko made like this in the parallel universe? It's clear that Yuki did not alter personalities, only altered events and removed the supernatural. In the case of herself and Ryoko, they wound up with personalities closest to how they acted as aliens: Shrinking Violet...and Stepford Smiler Knife Nut.
 * The troper writing this secondary theory has considered this interpretation canonical for a while (to the point of mentioning it on the Cast Page), but it's left ambiguous enough by the narrator (who had more important things to worry about, like bleeding to death) that it probably belongs here.
 * There's a doujin that I believe is entitled All-Purpose Cultural Yuki Nagato based on this idea, with the twist that Ryoko is actually in love with Yuki (in her psychotic way), and also explains why the alternate Yuki still wears glasses when Kyon has told her she looks better without them (Ryoko thinks she doesn't). It's a bit explicit, though.
 * Alternately, Alter-Ryoko appeared because Yuki STILL HAD Haruhi's powers, and summoned her when Kyon TRIED TO SHOOT HER WITH A GUN! Yuki however didn't know she have been granted those power.
 * Alternatively, Alter-Ryoko helped Yuki change the world, and was near her when it happened. Retaining her own memories, Ryoko was there to protect Yuki because Yuki would no longer be able to protect herself. She was an ordinary human now. It was only natural that Ryoko attacked Kyon when he pointed at Yuki with a gun. In the first chapter of the 7th novel, Ryoko asks the future Yuki (who saved Kyon from Ryoko): "Why? Wasn't this what you wanted?"
 * Alter-Ryoko couldn't be her subconscious desire since Yuki was conscious of that desire, but it was her defense mechanism to try to preserve her life of normalcy with Kyon. The gun was possibly a symbolic choice on Yuki's part, since it would kill off not just the Alter-Yuki she wanted to be, but would leave Yuki vulnerable to termination by the IDSE for reality-warping in the first place.
 * It's possible that when Yuki recreated Ryoko, she didn't think to alter her personality like she did her own, so even though Ryoko was now human, she was still acting as Yuki's "back-up unit".

Nagato could hijack Haruhi powers because Kyon transfered them to her
Nagato was able to use Haruhi powers to alter reality in Vol.4 only because Kyon - probably subconsciously - transfered Haruhi power, or allowed them to be transfered. Tachibana Kyoko thinks that Kyon can transfer Haruhi power to Sasaki - or at least is crucial in doing so. Some dialogs in Asahina Mikuru's Adventure suggest that Kyon is somehow 'key' to Haruhi power. Of all people in the world, who Kyon trust most and wouldn't mind if they were holders of supernatural powers? Nagato.

Kyon is unconsciously a genie, and grants the wishes of those closest to him
Several of the above WMGs relate to this, but this is different in an important way: Kyon grants wishes, but not his own. At least not directly. Nagato, a sci-fi bookworm wanted to know everything and be an alien. So she's turned into an Integrated Thought Sentient Entity interface, which knows pretty much everything AND is an alien. Koizumi is classy, and given his bootlicking personality he wants to be high up in some organization. So, he's given the most important job an esper can have, and Haruhi considers him her second in command. Asahina's motives are unclear. (And this troper personally believes the WMG that she's only helpless to get close to Haruhi and Kyon) Since she's very secretive, I suppose her wish would be that she gets to be "in the loop". Notice that she also refuses to tell people things that she knows they already know. Either that or she wants to know her current problems will get better in the future, which she knows becuase she has seen her future self. Lastly Haruhi, who just wants to be special. If Kyon really does care about Haruhi, then he's made her the most important person in the world, with more than three organizations all wanting to know more about her, yet all subservient to her wishes. Now Kyon never gets his wishes unless someone else helps him out. The only problem is that other people that are somewhat close to him don't get any abilities, or else Taniguchi would be the most popular guy in school. It also seems that Kyon's sister doesn't have any wishes. On the other hand, Kyon's sister gets a magical cat in the books and is allowed on the island in the anime. Another problem is that Ryoko Asakura got a wish granted, and she definitely doesn't seem to be a special person of Kyon's, unless Nagato wished to save Kyon.
 * Kyon equals Ayu, uguu? My mind is shattered!

Yuki doesn't really want to be normal.
Kyon thought he did, but realized he was wrong when he actually had the choice. Alternate-universe Yuki didn't have the chance to properly consider it, since she didn't know what her alien self had done to change things. For all we know, she would have come to the same realization as Kyon. (I don't expect this guess to be popular, since it makes her much less The Woobie.)
 * I can agree with her not wanting to be normal. Isn't the implication that she just wants to get away from Haruhi who is annoying the hell out of her? She can't even express her annoyance properly to anyone but Kyon! Remember, this is mostly before Haruhi's character development where she's dragging everyone around, dressing them up, groping them and generally making life very difficult for someone who would like to just sit around and read without being interrupted. She wants to be special in more normal circumstances (read: an off switch for when it gets to be too much. Alternate reality Yuki had some overlap in personality and interests, but she wasn't the same and probably really would have just preferred normalcy.
 * I read this differently; Errant Nagato does want to me normal, desperately. She does everything within her power to ensure her past self can't interfere. (The sync-preventing barrier, making Asakura essentially her bodyguard, etc.) This turns the events of the book into something of a giant chess match between Past Nagato and Errant Nagato. Kyon assumes his awareness of the change and the hints along the way are Nagato wanting him to be the one to make the final decision, but I think they were the direct result of Past Nagato's tinkering, and she didn't give a damn what he thought, she just wanted out.
 * The question isn't "does she want to be normal", but "does she want to be one of those weird alien creatures on the planet she's investigating."

Yuki is the real/original reality bender.
It's clear that Yuki has the most power out of the three helpers, and she apparently steals Haruhi's powers once. As a sci-fi aficionado, she always wanted to be an alien, and the Integrated Data Sentient Entity isn't very stock as aliens go, it's quite well thought out. She probably lost control of her powers once before, so she buried her emotion with her powers. It's possible the relationship with her Nakama is her way of making sure it doesn't happen again, so that she can restore her own emotions. Asakura was shocked with her coding ability, - which is apparently above normal - to save Kyon, and of course, it was very dramatic. It may also be possible when Haruhi was destroying the world that it was Yuki's jealousy, since Haruhi doesn't go anywhere near as out of control when she's jealous of Yuki. Yuki constantly bails out Kyon of situations she creates because she wants to be useful. As for Asahina, she was probably created to give Kyon something to look at without objectifying herself. Itsuki was brought in because of his tendency to speculate and help Kyon figure things out, or to divert things.

Haruhi's presence could be a result of any number of things: Kyon's presence is obvious. She found a normal person, for whom she will do anything. She grants his earlier wish to meet time travelers, espers and aliens. She's given him something to do, and she's made him rely on her. Yuki has been characterized as being burdened by the knowlege of what is to come, and that is to make sure she is not going to destroy everything.
 * An avatar through which to manipulate events and bring them together.
 * A person to give the powers to, as something fun to do through conflict
 * A curiousity endeavor, as in, how do people respond to omnipotence?

Yuki is going to die in the tenth book.
Then, Haruhi will finally find out about the web of secrets around her. And then she shall bring down divine fury on the people who dared harm a Brigade Member. There are plenty of ways that she could find out, but the one I'd like the most: immediately after Yuki passes on, Kyon turns to Haruhi, plays his trump card, explains the situation, and sits back to watch the fireworks.
 * I doubt Kyon would wait for Yuki to actually die. If it becomes clear that she's going to die and the rest of the Brigade has no solutions, he has every reason to play it preemptively.
 * Remember, the Trump Card is the Forbidden Chekhov's Gun. Basically if both Koizumi and Mikuru are ALSO neutralized, there would only be one person left for Kyon to call help from: Haruhi Suzumiya.
 * Neutralized or not, what could Koizumi or Mikuru possibly do to help against an enemy capable of neutralizing Yuki?
 * I don't quite get the 'trump card' thing. If Yuki can hijack Haruhi's power to make"Disappearance", it follows that her superiors can hijack them as well. So much for the 'trump card'.
 * Kyon never told any of the interfaces the nature of the trump card (it seems he's only thinking it when talking to Yuki), so for all they know he's bluffing. They're unlikely to want to hijack Haruhi's powers without a very good reason, which means that unless they have an interface eavesdropping when Kyon plays the card the first they'll know about it is when the fully aware Haruhi comes for them, by which point it will probably be way too late.
 * Just because the IDE created Yuki doesn't mean it has all her powers. For example: Humans have created machines that can travel thousands of kilometers per hour, but humans themselves can't. Yuki has practically killed the IDE in Disappearance without it being able to prevent it, so why wouldn't Haruhi be able to do it too?
 * Jossed. She's alive and kicking through the eleventh.

Haruhi subconciously allowed Yuki to steal her power
It makes things more interesting, interesting enough for a movie. Thats why Kyon's trump card works-Haruhi will let her powers be used for things which are arguably 'fun', but removing one of her brigade members? No dice.

Haruhi is really Jesus' second human incarnation
She's testing if humanity is yet ready to go back to Eden now. By accepting someone as weird as the melancholical and bossy Haruhi, they would prove theirselfs to be worthy.

Yuki has thousands of masks and yukata hidden in a closet in her apartment.
It's possible that, since she remembers every summer in Endless Eight, that Yuki also kept all of the yukata Haruhi bought her and all of the masks Yuki bought herself. And, since each mask and yukata appear to be different, the time duplicate destruction is avoided.
 * Why would she still have the yukata and masks if time had been undone? They would not disappear, but would they not have gone back to where she got them at the reset, and stayed there or been taken by another person when she got different ones? Otherwise, they are coming from nowhere. And most importantly, isn't it gross misconduct for Yuki to expand her closet just to have enough space for all those sets of robes?
 * Gross misconduct? Why would the Integrated Data Entity care how big Yuki's closet is?
 * That was the joke.
 * Unless she got her hands into TARDIS technology. Which is probable.

Yuki does in fact have emotions, but only Kyon can see them.
I have not read the novels, but Yuki expresses emotion three times that I know of: happiness during the Day of Sagitarius, anger during the Ryouko fight, and boredom during Endless Eight. Mikuru and Itsuki know she's an alien so they don't bother to look for signs of emotion, and Haruhi is, of course, completely oblivious.
 * I believe the way it works is that Kyon's the only one perceptive enough to notice. Her emotional signals are extremely minor compared to most people's, but Kyon's learned how to tell how she's feeling.
 * I think he's wrong about half the emotions he reads from her. We simply accept what Kyon says she is feeling? Since when has his track record at reading people been any good?
 * If you disregard his rather extreme Selective Obliviousness about Haruhi's feelings for him, since always.
 * According to him. Not to be get too geeky here, but uh you can think of it like Shamisen was saying. His interpretation of how Yuki etc. feel is simply a scenario that matches the evidence so far. Just like Koizumi and Mikuru's theories do, despite being completely contradictory. In fact, Kyon's perceptions drastically color ours. The most notable counterexample would be in his refusing to be suspicious of Mikuru, which was pointed out by Koizumi.

Nagato broke her directive of "observation" and hooked up with Kyon during one or more iterations of Endless Eight.
The "errors" accumulating due to uptime far longer than her original design specification, along with frustration at her powerlessness to end the endless summer, drive Nagato to act out by sleeping with Kyon. Kyon does not remember, but is aware of something "changed" in Yuki, while Yuki cannot forget, but also cannot do anything about her newfound feelings, as Haruhi's jealousy would cause The End of the World As We Know It. As a result, she creates an Alternate Reality where Haruhi is out of the picture, she can be a normal human free of the burden of her duty and memories, and she and Kyon can get to know each other and fall in love. The one memory she leaves herself of her old life is also the moment when she first became attracted to Kyon out of more than just intellectual curiosity (though she did not realize it until later): the episode at the library earlier that year.

Additionally, Nagato does not truly give Kyon an option out of I Want My Beloved to Be Happy; rather, she is thwarted only by the foresight of her earlier, coldly logical self, who does not understand the feelings that she will come to experience later on. This only adds to the angst that runs beneath her Emotionless Girl exterior.

Yuki was the one responsible for Endless Eight
It was a last ditch attempt to prevent Disappearance from happening.
 * Or at the very least she took no action to prevent spending six centuries beside her love.

Haruhi subconsciously "remembers" Nagato taking her power, and recreated "The Vanishment of Nagato Yuki Chan" world for her AU self.

 * Behold: Exibit A. She appears before Yuki-chan the same way John Smith did to her; to get her to join the Literary Club.
 * Actually, this is the Haruhi from that world (hence the hair-style and ribbons). After "our" Kyon left; the power flowed from that Nagato to her; and she had already been told about her alternate universe having those powers by "our" Kyon; so she acknowledged it immediately. First order of business was to clean things up.

Yuki didn't steal Haruhi's powers
I never really bought the whole stealing powers thing to begin with. It was left too vague and I think if she'd had that ability she'd have used it during the Endless Eight. Nevertheless I accepted it because we had nothing else to go on, until book nine. It showed the powers were transferable and the implication seemed to be that the powers currently reside in whoever Kyon wants to be with on a subconscious level. First it was Sasaki then Haruhi. The point at which Yuki "obtains" the powers is Disappearance, which also happens to be the point at which the narrative (written by Kyon) starts focusing on Yuki instead of Haruhi, coincidence? I reckon that this is the point at which Kyon shifts affections to Yuki and Yuki suddenly finds herself in possession of the powers. Being an alien she actually realises she's got them, unlike the previous two owners, and uses them. The question is, does she still have them?
 * Don't forget, though - she didn't use her powers during Endless Eight because she was instructed only to observe. I don't doubt that she seriously wanted to jack Haruhi's powers and end her boredom, but that would go against her orders.
 * I get the feeling she didn't do anything there because, if you'll notice, nobody ever asked her to do anything. Not even remind them that they were in a loop. She rather seems to lack initiative. Until Disappearance, anyway. Also, the IDE has shown itself to be perfectly capable of 'data manipulation.' It's likely they only need Haruhi because of how chaotic she is: She does things they would never think of. Perhaps she just stopped following a sort of non-interference order and showed what she was really capable of.
 * The Data Entity is a Reality Warper, yes. However, the reason it is watching over Haruhi is because it is limited by Equivalent Exchange. They can manipulate data all they want, but only Haruhi can create (and presumably destroy) data. Yuki mentions this in her first exposition.
 * Ok then, but if only Haruhi's power is capable of that, and Yuki can steal that power, why bother observing her? What Yuki did is right along the lines of what Haruhi was trying before Kyon possibly interrupted her. There's just too big a plot hole to say she stole the powers and leave it like that. If that were the case, the IDE would simply snatch the powers, withdraw Yuki etc. and go on their merry way. If they're still watching Haruhi, there has to be more to it than simply data creation.

Yuki gave Haruhi her powers three years ago on behalf of the IDE.
The IDE always had such reality warping powers and simply couldn't think of a way to use them to improve itself anymore. They decided to give someone else their abilities and see what they would do with them. So they picked a race they were interested in, humans, and then narrowed down the choice to Haruhi because A. she wants weird things, B. she's secretly rational and won't notice and threaten them and C. She's a decent person deep down and won't do anything too dangerous. Yuki could steal her powers because she gave them to Haruhi in the first place. It's why she was around three years ago. It's also why her abilities can involve reality warping as well, such as changing the baseball bat to always hit home runs. When she went on a rampage after stealing said powers, the IDE didn't punish her not because Kyon threatened them, but because they would lose Kyon's support and influence over Haruhi and therefore an external factor introducing major changes. She finally started doing weird stuff, after all. Finally, perhaps Haruhi isn't the only one with weird reality warping powers and this is all a giant experiment the IDE is carrying out. They grant these powers and take them away again if they're not learning anything from the wild chaotic humans, like Sasaki's insistence on normality.

Yuki was programmed to have an emotional bug
The IDE is a super intelligent entity with access to near unlimited computing power. It would not make an error of that magnitude in such an important program. The error was programmed in intentionally by either the IDE or Yuki herself as Xanatos Roulette of currently unknown purpose. Alternatively the emotional bug was the result of Yuki, tired of serving the IDE after the Endless Eight loop, was able to escape its control. They engaged in a data war similar to the one in Snow Mountain Syndrome, and the result was the alternate reality Kyon found himself in. The winner depended on whether Kyon succeeded at reversing the effect, although who actually won when he succeeded is unknown.

One or more characters is a Time Lord.
... is this just here to fulfill the 14th Example Law?
 * No. Mikuru is a time lord by virtue of the fact that she's a time traveller, and as we know from reading the WMG pages, all time travellers are time lords.

Yuki ordered Ryoko to attack Kyon.
To be trusted by Kyon, Yuki told Asakura to atack Kyon so that Yuki could save him. If Asakura really was trying to kill someone, im pretty sure that there are better ways that trying to kill him with a knife. And this can be match with the "Kyon is god". Think about it, Asakura was trying to kill Kyon to watch what Haruhi do, but if Kyon REALLY is God, she attacks him to see what God can do. This would explain why she chose the Knife Nut option, to get the maximum emotional response. Yuki kept to her plan though.

The events of "Disappearance" are directly due to Yuki developing romantic feelings for Kyon.
The way her new, "normal" world was set up made things quite easy for her in that regard:
 * Haruhi was at Kouyouen with Koizumi, who already had a crush on her - both placing her at a distance from Kyon, and giving him a viable rival for Haruhi's affections.
 * Of all the former SOS Brigade members, Kyon could most easily establish contact with Yuki. Mikuru was an upperclassman with a protective best friend, Haruhi and Koizumi were students at another school, but Yuki was just a shy girl who was attracted to Kyon and wanted another member for her literature club. She also had the most positive (well, the least negative) initial reaction to him.
 * Yuki let Kyon keep his memories and gave him the ability to change the world back. As much as she wanted the chance to have a normal relationship with him, she didn't want to do it against his will - she wanted him to be happy.

Yuki did not leave Kyon with his memories intact because She Wants Her Beloved To Be Happy
She did it because she knew that he was the only one capable of choosing the "strange" real world over the "normal" false one. Yuki does not exist in time and space the exact same way as we do. Because of the "synchronization" of her past and future selves she, like Dr. Manhatten, experiences her entire existence simultaneously. She knows exactly what she's going to do but is powerless to stop it, it will happen, because it must happen, because it has happened. Mikuru and Itsuki by admission and evidenced by their actions would prefer quiet ordinary lives, and Haruhi cannot carry it out because she is clueless to the situation (and might not even notice the change in the first place) and not focused enough to figure it out before the deadline anyway. Not only is Kyon the only one capable of choosing the old world knowing full well the responsibilities that come with it (having already done it once before in Melancholy), he's also the only one capable of taking the action necessary to see it through to the end, to the point of mobilizing the future versions of the himself and the SOS brigade to come back and save his own life when he's injured. He was not given a choice, he never had a choice because there was never any doubt which course he would take. He was given a job to do and he performed it. The moment he finds the bookmark there is absolutely no doubt about what will happen. Hell, in the movie version at least she comes right out and tells him this is why he was left with his memories intact, because he was the only one who could and would stop her.

Nagato drugged the tea she gave Kyon the first time (storywise anyway) she invited him to her house.
All the weird backdrops are Kyon tripping the hell out.

Kyon’s mission to find the keys in the Disappearance arc was meant to be a lot harder.
Kyon learned which school Haruhi went from Taniguchi. Taniguchi is supposed to be absent like other former East Middle school students. Yuki didn’t consider the fact that Taniguchi’s father would force him to go to school with a high fever. Kyon is supposed to find Haruhi by himself.

Yuki is aware that the Five-Man Band will destroy the world.
She does the minimal possible in Disappearance to move all the members away from each other and is thwarted when the IDSE overrides her common sense to impose the "interesting" event that will doom the world. Mikuru is from the end of the world and has been sent back to mix things up in random ways (making her seem rather stupid) in a vain attempt to save the Earth from the coming doom.

Yuki Nagato is human.
Yuki was born to a Mr. and Mrs. Nagato and was attending North High until Haruhu jacked Kyon into the first data explosion. At that point the IDSE infected Yuki and froze her in place to await Haruhi's entry into that school. When Yuki blocked out data manipulation she didn't become human, she just became uninfected. Thus Ryoko's comment about Yuki's puppet master, etc.

Yuki didn't steal the power, she moved it.
The resolution at the end of The Disappearance was not complete because some of the power remained with Sasaki. Note how the anti-SOS pops up shortly afterwords and in a very immature condition, from which they rapidly evolve to be a match for the SOS brigade.

The series will end exactly like the first Star Trek movie.
Yuki and Haruhi merge.

Miss "Gate Length" is the result of Moore's Law gone wild.
Hence her family name. See: gate length defined.

708 is just as meaningful as 505.
Now, has this already happened, or will it happen?
 * Flip it over and it becomes BOL or "Be On the Lookout".

Human Yuki is not powerless.

 * Instead she's a Papermaster.

Yuki is the only person out of the three supernatural SOS members telling Kyon the complete truth.
Her organization are only observing for the time being, and as of yet don't see any reason not to tell Kyon the information he asks for - even moreso now they know that Kyon can easily give them a hard time if he needs to. Yuki only warned him about her perhaps lying to him incase her superiors ever change their mind.

Yuki shot first!

 * The great Kuyou/Yuki war started at the same moment that Kuyou realized that she was going after the wrong boy? How about it started just before X-mass?
 * Kuyou: "Where is Kyon?"
 * Yuki: "See that boy right over there? He's your man."
 * Kuyou: "Thank you."
 * Yuki: "Now excuse me while I change the Universe."
 * Kyon took the two-day limit the wrong way around. Yuki was asking for two days in order to totally throw Suou off, not limiting the change the two days.

Yuki is a tool left by Neglectful Precursors
How can a life form not evolve? The answer is that Yuki's patron is NOT a living being. It did not evolve over time. It was created in its current form by others some time ago. Yuki is a Berserker. She has forgotten her role in eliminating the previous civilization and is now looking for some goodlife on Eatth.

Yuki is using Kyon's brain.

 * She said the cricket was using somebody's brain to increase it's probability of existence and that this was a related life form.
 * She said that humans hold the key to the evolution of her kind.
 * The interfaces have been very selective about lobotomizing espers, only taking out those who can't handle the truth.

Alt-Yuki was lying about not being a writer.
The files she deleted from her PC were the fanfics she had written about her being a Mary Sue alien engaged in fun adventures with the boy from the library. (Once he walked into her clubroom, these were no longer needed.)