The book begins with Miles Halter leaving his home in Florida to attend the Culver Creek boarding school in Birmingham, AL. Miles arrives at the school as a smart but lonely junior, and he is determined “to seek a Great Perhaps.” At school he befriends Chip (also known as the Colonel), Alaska, and Takumi, each of whom have a special talent—memorizing facts about other countries, quoting poetry, and freestyle rapping, respectively. Miles is obsessed with famous people’s last words, and Alaska introduces him to the last words of Simón Bolívar, who died wondering how to “escape the labyrinth.” Alaska is often exciting and wild, but she can also be moody and withdrawn. Miles spends a lot of time trying to understand her better, although he makes little progress. Overall, however, he is thrilled to finally have friends.
In addition to making friends for the first time in his life, Miles spends much of his time at Culver Creek learning to break the rules. His friends encourage him to smoke and eventually he drinks on campus as well. When Miles first arrives on campus, Kevin and Longwell, two Weekday Warriors (wealthy kids who don’t board at the school), pull him out of bed in the middle of the night, wrap him in duct tape, and throw him into the school’s lake. The Colonel is furious about this, and he and Alaska work on a plan to get back at them. Over time, the group discovers that Kevin and Longwell thought that the Colonel had ratted to the Eagle, the dean of students, about two students named Marya and Paul. Marya used to be Alaska’s roommate, but she and Paul were caught smoking pot after having drunken sex and expelled. Kevin and Longwell thus hurt one of the Colonel’s friends because they think he hurt one of theirs. Alaska’s desire to get back at the Weekday Warriors is exacerbated when they flood her room and ruin her “Life’s Library” of books she is saving to read.
For much of the first semester, how Marya and Paul got expelled is a mystery, but eventually Alaska tells Takumi that she reported them, and Takumi tells Miles. The Eagle caught Alaska breaking the rules and threatened expulsion unless she gave him information about other students. Takumi and Miles can’t figure out why Alaska would be so afraid of getting expelled that she ratted on her friend, because not ratting on anyone, no matter what they do, is the most important social code at Culver Creek. The Colonel is furious when he finds out that Alaska was responsible, because he takes loyalty very seriously.
Alaska and Miles spend Thanksgiving break on campus together, and then everyone goes home for Christmas. When they get back, Alaska, Miles, Takumi, the Colonel and Lara, whom Alaska thinks Miles should date, execute a prank on the Weekday Warriors. Takumi and Miles distract the Eagle by setting off fireworks around campus while Lara puts blue dye in Kevin’s conditioner and hair gel. Meanwhile, Alaska and the Colonel send fake progress reports with failing grades to a number of Weekday Warrior parents.
The next morning the group hangs out and gets drunk in a barn. They play a game called Best Day/Worst Day, in which each person tells the story of their best and worst day. Alaska’s worst day was when she came home from school and her mom collapsed to the ground and started shaking. Alaska was very young, so instead of calling 911, she sat with her mother until she thought she fell asleep, but in fact, she died. Alaska has never told anyone at Culver Creek that her mother is dead, and for the first time, Miles can understand why Alaska is so moody and impulsive. She is paralyzed by the memory of freezing when her mother needed her, so she compensates with constant action. Later that evening Miles and Lara start dating.
The next evening, Alaska and the Colonel get drunk to celebrate the success of their prank. Alaska dares Miles to make out with her. They do, until Alaska says that she is sleepy, and she asks Miles, “To be continued?” Everyone falls asleep until Miles and the Colonel are woken up by a hysterical Alaska. She enlists their help distracting the Eagle so that she can leave campus. Miles and the Colonel have no idea why she is upset or where she wants to go, but they distract the Eagle long enough for her to leave.
The next morning the Eagle announces to the school that Alaska died in a car crash the night before. Miles and the Colonel spend much of the rest of the year trying to deal with their grief, hoping to figure out why Alaska left and whether she intended to kill herself or not. Miles and the Colonel get into a number of fights, and both fall into a depression, though his World Religion class helps Miles come to terms with what occurred. Eventually the friends decide to memorialize Alaska by pulling the prank she had planned for their senior year. A few days later, with Takumi’s help, Miles and the Colonel realize that the night Alaska died was the anniversary of her mother’s death. Alaska had forgotten to put flowers on her mother’s gravestone, and so she had drunkenly driven off with that purpose. Miles ends up deciding that he doesn’t care whether or not Alaska committed suicide in the end, because he loves her no matter what. The novel concludes with Miles returning to his quest for the “Great Perhaps” and deciding that forgiveness is the best way out of “the labyrinth of suffering.”