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Miles Halter is tired of his predictable and friendless life (check out the going-away party for him at the beginning of the book), so he decides to attend Culver Creek boarding school in Alabama for his junior year of high school. He tells his parents that he's going to seek a Great Perhaps, that there's something more for him.
And there is. The story is split in two parts: before and after.
Miles meets the Colonel (real name Chip Martin), Takumi, and Alaska Young. The Colonel grew up in a trailer park, Alaska and her dad don't get along (mystery alert), and Takumi is just kind of there for a while. The three take Miles (nicknamed Pudge because he's so skinny) under their wing and introduce him to the social order of campus, mischief-making, smoking cigarettes, and drinking. They have to avoid the Eagle—the aptly-named dean of the school—when they're creating mischief so they don't get brought before a peer jury and appropriately punished.
Miles's favorite class is religious studies, taught by an old man nicknamed… the Old Man. He lectures all the time and makes Miles think about religion, philosophy, and life, and Miles loves it. Alaska doesn't.
After Miles is hazed pretty hard by the Weekday Warriors (students who stay only during the week at the boarding school), his new friends vow to help him return the favor. Miles meets Lara, and goes on a triple date with her, the Colonel and his pseudo-girlfriend Sara, and Alaska and her college-aged boyfriend Jake. The date ends with Miles getting a concussion from a basketball and ralphing on Lara's shoes. Also, the date doesn't really mean anything, because Miles is well on his way to falling in love? lust? some combination? with Alaska.
Time passes and Miles continues his involvement in shenanigans and obsessing about Alaska. He stays on campus for Thanksgiving to try to get with her, but all he gets for his trouble is a sense of homesickness and confusion. Miles, the Colonel, Takumi, Alaska, and Lara pull an epic prank on both the Eagle and the Weekday Warriors that involves blue hair dye and fake progress reports, and during their hideout, all the friends find out that Alaska's mom died of an aneurysm right in front of Alaska when Alaska was eight… which explains a lot about Alaska.
A couple nights later, Miles and the Colonel and Alaska are hanging out in Alaska's room. Both the Colonel and Alaska are drinking to celebrate the epic prank, but Miles isn't. Alaska and Miles make out a little (dream come true moment for Miles), but then Alaska gets a phone call from her boyfriend Jake because it's their eight-month anniversary. Ooh—drama. Then she freaks out and leaves campus in her car. Miles and the Colonel help her go by setting off fireworks on the Eagle's porch.
All students are called to the gym the following morning for an announcement. The Eagle says that Alaska has died in a horrible car crash. Emotional train wreck ensues for all students… but especially for Miles and the Colonel.
The Colonel and Miles are consumed with guilt. They flail about with each other, in classes, and with their other friends because they are caught up in how Alaska died, their culpability, and whether or not she committed suicide.
The two friends try to unravel the mystery: they go to talk to the officer whose car Alaska hit, they steal a Breathalyzer from the Eagle's house to figure out how drunk Alaska actually was, and they talk to Alaska's ex-boyfriend, Jake. In the midst of this, they ignore both Takumi and Lara (she and Miles dated for like, a day). And at the same time, Miles is trying to come to grips with who Alaska was and who he wanted her to be.
Then Miles and the Colonel, with Takumi and Lara (who have forgiven them for their single-minded grief), plan the most epic prank ever seen by Culver Creek Boarding School. It involves a class speaker, a stripper, and a lie told by Miles's father. Dedicated to the memory of Alaska, it is a huge success.
Life marches on. Eventually Miles and the Colonel come to terms with their loss and grief and give up on the mystery of Alaska; then they throw themselves into their studies. The Old Man assigns a final exam essay that asks how each student personally gets out of their own labyrinth of suffering. Miles, finally, has some answers for the question and writes about them in his final exam, thus writing himself out of his own labyrinth of suffering about Alaska.