On October 2, 1988, in the small town of Middlesex, Virginia, troubled teenager Donnie Darko, led by a mysterious voice, sleepwalks out of his home. Once outside, he meets a figure in a monstrous rabbit costume who introduces himself as Frank and tells Donnie that the world will end in 28 days, 6 hours, 42 minutes and 12 seconds. Donnie wakes up the next morning on a local golf course and returns home to discover a jet engine has crashed into his bedroom. His older sister Elizabeth tells him the FAA investigators do not know its origin.
Over the next several days, Donnie continues to have visions of Frank, and his parents, Eddie and Rose, send him to psychiatrist Dr. Thurman. She believes he is detached from reality and that his visions of Frank are “daylight hallucinations”, symptomatic of paranoid schizophrenia. Frank begins to influence Donnie’s actions through his sleepwalking episodes, including causing him to flood his high school by breaking a water main. Donnie also starts seeing Gretchen Ross, who has recently moved into town with her mother under a new identity to escape her violent stepfather. Dr. Thurman hypnotizes Donnie at his next therapy session, but it ends with him discussing his sexual fantasies involving Christina Applegate while he unzips his pants, causing Thurman to end the session prematurely. Later, Donnie goes to a clearing and shoots bottles while his friends discuss the sexual components of Smurfs.
Gym teacher Kitty Farmer attributes the act of vandalism to the influence of the short story The Destructors, assigned by dedicated English teacher Karen Pomeroy. Kitty begins teaching “attitude lessons” taken from local motivational speaker Jim Cunningham, but Donnie rebels against these, leading to friction between Kitty and Rose. Frank asks Donnie, who in turn asks his science teacher, Dr. Kenneth Monnitoff, if he believes in time travel. Monnitoff gives Donnie The Philosophy of Time Travel, a book written by Roberta Sparrow, a former science teacher at the school who is now a seemingly senile old woman living outside of town. Later, while watching football, Donnie notices bubbly columns emerging from the chests of people around him that show Donnie where the person will move. A bubble appears on his chest and he follows it to his parents’ closet where he finds and takes a gun.
Kitty arranges for Cunningham to speak at a school assembly, where Donnie insults him. He later finds Cunningham’s wallet and address and Frank suggests setting his house on fire. Firefighters discover a hoard of child pornography there. Cunningham is arrested, and Kitty, who wishes to testify in his defense, asks Rose to take her place as chaperone for their daughters’ dance troupe on its trip to Los Angeles.
With Rose and little sister Samantha in Los Angeles, and Eddie away for business, Donnie and Elizabeth hold a Halloween costume party to celebrate Elizabeth’s acceptance to Harvard. At the party, Gretchen arrives distraught as her mother has gone missing, and she and Donnie have sex for the first time. When Donnie realizes that Frank’s prophesied end of the world is only hours away, he takes Gretchen and two other friends to find Sparrow. Instead, they find two high school bullies, Seth and Ricky, trying to rob Sparrow’s home. Donnie, Seth, and Ricky fight in the road in front of her house, just as she returns home. Ricky and Seth flee when an oncoming car runs over Gretchen, killing her. The driver is Elizabeth’s boyfriend, Frank Anderson, wearing the same rabbit costume from Donnie’s visions. A second Frank can also be seen standing in the bushes in the same scene. Donnie shoots him in the eye with his father’s gun, and walks home carrying Gretchen’s body.
Donnie returns home as a vortex forms over his house. He takes one of his parents’ cars, loads Gretchen’s body into it, and drives to a nearby ridge that overlooks town. There, he watches as the plane carrying Rose and the dance troupe home from Los Angeles gets caught in the vortex’s wake, which rips off and catches one of its engines. Events of the previous 28 days rewind. Donnie wakes up in his bedroom, recognizes the date is October 2, and laughs as the jet engine falls into his bedroom, crushing him. Around town, those whose lives Donnie would have touched wake up from troubled dreams. Gretchen, who in this timeline had never met Donnie, bikes by the Darko home the next morning and learns of his death. She and Rose exchange glances and wave as if they know each other but cannot remember from where in a moment of déjà vu.