The Disappearance of Haruhi Suzumiya is the fourth book in the Haruhi Suzumiya light novel series, taking place during December (mostly) of Kyon and Haruhi's first year of high school. The story has been adapted into an animated film of the same name, released in Japan on February 6, 2010. Another one of the series' time-travelling stories (there are a lot of them), it presents perhaps one of the most convoluted stable time loops of any of them. It has been consistently cited as the favourite book in the series by a great number of the fans, probably due in no small part to the absolutely moe treatment given to alternate-Yuki.
Kyon wakes up on December 18 to find that Haruhi and Itsuki are missing and the other members of the SOS Brigade don't know who he is. Additionally, Yuki acts like a normal girl. As if that weren't enough, Asakura shows up to class, despite having "moved to Canada" earlier that year after trying to stab him. He attempts to find his friends, but as he either can't find them or they don't recognize him, it seems useless. He finds Yuki in the Literature Club's room, and after thoroughly freaking her out with his crazy alien talk, she shyly asks him to join her club as he is about to leave.
While in the clubroom the next day, Kyon finds a book Yuki once lent him (The Fall of Hyperion by Dan Simmons). In it is a bookmark with the message: "Program run condition: collect keys. Deadline: two days."
Yuki timidly invites Kyon to her apartment, where he realizes that she does have one memory of him. From Kyon's perspective, they once visited a library together where he helped Yuki obtain a library card as he quickly tried to shoo her outside to where Haruhi was demanding their presence. As this new Yuki remembers it, however, he was a random stranger who helped her get a library card when she didn't know what to do.
Asakura arrives, causing Kyon to attempt to leave prematurely. As he turns to leave, Yuki tugs lightly on his sleeve with the oh-so-cutest please-don't-leave look on her face you ever did see, and he gives in. He learns that in this new world, Asakura is simply Yuki's friend and neighbour and will most likely not try to stab him again. Most likely.
Kyon mentions Haruhi during PE class, and his friend Taniguchi (who still remembers him) recognizes the name, as the two went to junior high school together. He tells Kyon she went to Kouyouen School after junior high, so Kyon skips school to go there. There he finds not only Haruhi, but Itsuki as well. He tries to talk to her but like nearly everyone else, she doesn't recognize him. He realizes that like Yuki, she will have one memory of him: he tells her what he did on Tanabata three years ago, and that he is John Smith (you should have read this first, you know). This gets her attention, and she listens to Kyon about how in his reality, Yuki is an alien, Mikuru is a time-traveller, Itsuki is an esper, and Haruhi has strange powers. Haruhi's interest is piqued, and she decides to meet the other Brigade members. Borrowing Kyon's PE uniform and pretending to be from the Student Council, Haruhi pulls Mikuru out of the calligraphy club and brings her to the literature clubroom where everyone else is waiting. As soon as they are all in the room, the computer flicks on and displays a message:
YUKI.N>If you are reading this,
I am probably no longer myself.
YUKI.N>When this message appears,
it means that you, me, Suzumiya Haruhi, Asahina Mikuru and
Koizumi Itsuki are all present.
YUKI.N>That is the key.
You have found the answer.
YUKI.N>This is the Emergency Escape Program.
To activate it, press "Enter",
otherwise, press any other key.
If you activate it,
you will be given a chance to repair the spacetime continuum.
However, there is no guarantee of success.
There is also no guarantee of your safe return.
YUKI.N>This program can only be started once.
Once executed, it will be erased.
If you choose not to activate it, it will also be erased.
Translation courtesy of Mazui subs
Naturally, he activates it. The program takes Kyon back to Tanabata three years ago (you really should read this first), where he again encounters the adult version of Mikuru, who had been expecting him. They go to Nagato's apartment where he realizes that the other him from this time and the young Mikuru are still frozen in time in the other room. Yuki explains that at some point three years from now, someone will change reality to one in which weird shit doesn't happen. She tells them to travel back to the future to right after this change occurs, and fire a magic needle gun at the person responsible, which will activate a restoration program, returning the timeline to normal. The one who altered reality is revealed to have been (or rather, will have had been going to have been) Yuki herself.
Back in the future, Kyon and Mikuru watch as Yuki alters reality. After she finishes, they approach her and Kyon raises the gun. And that's when Asakura comes out of nowhere... and stabs him. You'd think Yuki would have learnt from past experience and made this Asakura not so stab-happy as the original, but there it is. Suddenly Yuki, having returned to normal somehow, stops Asakura from delivering the finishing blow. As Kyon lies on the ground, nearly unconscious, two Mikurus crowd over him, crying. A "mysterious" figure (who is obviously a future Kyon) is revealed to be the one who saved the day, and narrator-Kyon blacks out.
Kyon wakes up in the hospital, where he's been asleep for three days. The other brigade members had been taking turns watching him, aside from Haruhi, who hadn't left his side at all. He finds out he fell down the stairs and dreamt the whole thing. OR DID HE? He didn't. Kyon decides that eventually he'll have to go back to that time again, to save himself... but not quite yet.