This novel for young people chronicles the eventful first year at private school for teenaged Miles Halter. As Miles makes new friends and discovers an interest in philosophy, he also discovers important answers to fundamental questions of human existence and equally fundamental truths about the natures of both loyalty and love.

The novel begins with a prologue-like description of a poorly attended going away party thrown for Miles by his well-meaning mother. After the sort-of party has ended, Miles explains to his parents why he wants to attend boarding school - not because he has so few friends, as his mother suggests, but because he wants to experience more of life.

After being dropped off at his new school by his parents, Miles meets his commanding roommate Chip and Chip's playful, attractive friend Alaska, both of whom introduce Miles to the ways of the school. That night, Miles is hazed by a group of wealthy kids whom Chip refers to as the Weekend Warriors, a hazing that goes beyond the usual ritual hazing of newcomers to such a degree that Chip believes something else is going on, and vows revenge.

As Miles starts classes, he discovers that he has an early favorite - World Religions, taught by the elderly and demanding Dr. Hyde. He also discovers that the rivalry between the Weekend Warriors and full-time boarders like Chip, Alaska and himself is quite intense, and has been going on for some time. Meanwhile, his friendship with Chip and his attraction to Alaska both intensify, and he makes new friends with Japanese student Takumi and Rumanian student Lara.

Chip and Alaska formulate a plan for taking revenge for the Weekend Warriors' attack on Miles and a subsequent attack on Alaska, calling on Miles, Takumi and Lara for help. The five friends soon enact their plan, hiding out in an old barn while they wait for the effects of their prank to dissipate. While there, they get drunk and, as part of a game to kill time, reveal important secrets about their lives. Also at this point, Miles and Lara get a little physical with each other and decide that they are boyfriend/girlfriend.

Following a visit to Chip's family at Thanksgiving and a visit home at Christmas, Miles comes to realize that his friendships at school are actually a kind of family. Meanwhile, he is becoming more and more attracted to Alaska, and increasingly intrigued by Hyde's lessons in World Religions class. One night, a drunken celebration in Alaska's dorm room ends with Miles and Alaska on the verge of making love when Alaska receives a telephone call that changes her mood completely and sends her rushing into the night, berating herself for always messing things up. The next morning Miles, Chip and all the other students at the school are told that Alaska died the night before in a traffic accident.

The grief stricken Miles and Chip both blame themselves for her death, and mount an investigation into what happened, searching out a police officer present at the scene of Alaska's accident, talking to her boyfriend, and wondering whether she committed suicide. Their grief and anger spill out onto each other, but a series of intense confrontations don't damage their friendship, and they ultimately come together (with Takumi and Lara) to commemorate Alaska's life with a major prank. Dr. Hyde, meanwhile, sets a pair of exams in which he asks his students to consider Alaska's life and death in terms of the philosophies he discusses in class. As a result of his investigations and his work for Dr. Hyde, the intensely grieving Miles eventually comes to terms with Alaska's death, realizing that what made Alaska special was something more than the sum of her physical, emotional, and experiential parts.