Miles “Pudge” Halter is the new student at the prestigious Culver Creek Preparatory School in Birmingham, Alabama. Unpopular at his old school, Pudge is nervous about making new friends, but he is immediately taken in by his roommate, Chip “the Colonel” Martin and introduced to his rag-tag group of friends, including Takumi Hikohito, Lara Buterskaya, and the beautiful, mysterious Alaska Young.
The night before school begins, Pudge is taken from his bed in the middle of the night, duct taped like a mummy, and thrown into the school’s lake. He survives and the Colonel promises revenge in the form of pranks against their rivals, the wealthy day students known as the Weekday Warriors. Early on in the semester Pudge is kicked out of his World Religion class for daydreaming and is admonished by his teacher, Dr. Hyde, for not being present in the moment.
As time passes, Pudge grows closer to his new friends. The Colonel is kicked out of every basketball game for jeering too much; Alaska tutors Pudge in pre-calculus; and the group is caught smoking by the dean of students, Mr. Starnes (known as the Eagle), at their favorite hangout spot, the Smoking Hole. An important element to the group's friendship is trust. Although Takumi reveals Alaska was the one who ratted out her roommate the year before and Pudge is unsure about trusting Alaska, he agrees to stay on campus with her for the Thanksgiving break. The two spend their time snooping through other students’ rooms, watching porn together, and eating Thanksgiving at the Colonel’s house with his mother.
When the students return from Christmas break, the gang plans their ‘pre-prank’ called Barn Night in which Pudge and Takumi set off a series of fireworks to lead the Eagle away from his house while Alaska send progress reports to some of the Weekday Warriors’ houses. To avoid getting caught, the group sleeps at the Smoking Hole where they discuss the best and worst days of their lives and Pudge gets his first kiss from Lara, despite his unrequited love for Alaska.
The return to campus is a triumphant one, with Pudge, Alaska, and the Colonel drinking while playing Truth or Dare. Pudge is dared to make out with Alaska and he complies, fulfilling his dream to be romantic with Alaska. Drunk and exhausted, Pudge and Alaska fall asleep in her room. Alaska awakens in the middle of the night to answer the ringing phone in the hallway. She returns in an extremely distressed state and begs Pudge and the Colonel to set off additional fireworks to distract the Eagle while she drives off campus.
The following morning, it is revealed that Alaska died in a car accident. Shocked by her death, Pudge and the Colonel stop talking to Takumi and Lara while they sort through their own emotions. With so many unanswered questions surrounding her death, Pudge and the Colonel begin an investigation. Reluctantly they allow Takumi to join and Pudge eventually makes amends with Lara, though they no longer date. After interviewing a police officer and Alaska's boyfriend who had called her that night, Takumi realizes that Alaska remembered it was the day after her mother's death while she was talking to Jake. Feeling responsible for her mother's death and distraught by the idea of having forgotten the day, Alaska attempted to drive to the gravesite. It remains unclear whether Alaska's death was an accident or a suicide. Pudge resolves his feelings for Alaska in his final essay for Dr. Hyde's class.
To commemorate Alaska's love of pranks and hatred of the objectification of the female body, the group decides to execute one last prank at Speaker Day. They invite a stripper pretending to be a professor of adolescent sexuality to speak at Speak Day. In the middle of the speech, Lara prompts the speaker to take off his clothes and begin to strip. The Eagle knows it was Pudge and his friends who hired the stripper but finds it to be a fitting way to remember Alaska.
In the end, Pudge is at peace with Alaska's death, knowing that he will never fully understand her, but that her memory will continue in the people she influenced.