Plot

Donnie and Elizabeth live with their parents Eddie (Holmes Osborne), Rose (Mary McDonnell) and sister Samantha (Daveigh Chase). Donnie is in therapy (he often wakes up outside the house not knowing how he got there) and is supposed to be taking his medications, which he stopped doing recently. Donnie and Elizabeth positively hate each other as siblings. Donnie is typically blamed for every wrong thing that happens in the neighborhood and is sick of defending himself.

On October 2, 1988, Donnie Darko (Jake Gyllenhaal), a troubled teenager living in suburban Virginia, is awakened and led outside by a figure in a monstrous rabbit costume, who introduces himself as "Frank" and tells him the world will end in 28 days, 6 hours, 42 minutes, and 12 seconds. At dawn, Donnie returns home (he was found sleeping on the golf course - and had the time coordinates written on his arm) to find a jet engine has crashed into his bedroom. His older sister, Elizabeth (Maggie Gyllenhaal), informs him that the FAA investigators led by Bob Garland (David St. James) do not know where it came from (as the matching serial number on the engine got burned and is unreadable). The family is shifted to a hotel till the house is fixed. Donnie is now a celebrity at school and hangs out with all the cool kids.

Donnie tells his psychotherapist, Dr. Thurman (Katharine Ross), about his continuing visits from Frank. Acting under Frank's influence, he floods his school by damaging a water main on October 6th, 1988 (24 days remaining). Principal Cole (David Moreland) has no option but to close down the school till it dries up. An ax was found embedded in a bronze sculpture (Of the Mongrel) on school grounds, with "They made me do it" written at the bottom of the sculpture.

Donnie also begins dating a new student, Gretchen Ross (Jena Malone), who has recently moved into town with her mother under a new identity to escape her violent stepfather. Donnie saves Gretchen from school bullies Seth and Ricky.

Gym teacher Kitty Farmer (Beth Grant) blames the flooding on the influence of the short story "The Destructors", assigned by dedicated English teacher Karen Pomeroy (Drew Barrymore). She says that in the story a bunch of kids destroy an elderly couple's house by destroying the water main from the inside and flooding it, exactly similar to what happened at the school.

Kitty begins teaching attitude lessons taken from motivational speaker Jim Cunningham (Patrick Swayze). Videos of Jim's lessons are shown to students during gym class. Donnie rebels against these motivational lessons (and tells her to shove the assignments up her behind), leading to friction between Kitty and Rose, Donnie's mother. Kitty gets Donnie suspended from after school activities for 6 months and tells Rose that she has significant doubts about her ability as a mother. Kitty and Rose's daughters are in the school dance troupe together.

On October 10th, 1988 (20 days remaining), Donnie asks his science teacher, Dr. Kenneth Monnitoff (Noah Wyle), about time travel after Frank brings up the topic, and is given the book The Philosophy of Time Travel, written by Roberta Sparrow (Patience Cleveland), a former science teacher at the school who is now a seemingly senile old woman. Donnie can't believe that the weird looking old woman he has run into several times (walking aimlessly and looking lost always) is a brilliant professor. Once Eddie and Donnie had almost knocked Roberta down with their car, and when Donnie went to help her, she whispered in his ear "Every living thing on the planet dies alone".

Donnie reads Sparrow's book in which she theorizes that a space time worm hole can occur in the event of a tangent universe, coupled with coming together of water and metal. If the conditions are there, the worm hole will form and rip a fabric through space time and will make itself known through the appearance of artifacts (like the jet engine). She says that the tangent universe cannot be sustained beyond a few weeks and will collapse in on itself destroying everything in it.

October 18th, 1988 (12 days remaining), Dr. Thurman tells Donnie's parents that he is detached from reality, and that his visions of Frank are "daylight hallucinations", symptomatic of paranoid schizophrenia. Donnie finds a life force emerging from his body that leads him to a gun in his father's closet. Donnie kisses Gretchen for the first time.

Donnie disrupts a speech being given by Jim Cunningham by insulting him in front of the student body, then burns down Cunningham's house on instructions from Frank. When police find evidence of a child pornography operation in the house's remains, Cunningham is arrested. During his hypnotherapy session, Donnie confesses his crimes to Dr. Thurman and says that Frank will soon kill someone.

Rose agrees to replace Kitty as chaperon for her daughter Samantha's (Daveigh Chase) dance troupe in Los Angeles, so Kitty can testify in Cunningham's defense. With Eddie in New York on business, Rose's older children are home alone.

Donnie and Elizabeth take the opportunity to throw a Halloween party to celebrate her acceptance to Harvard. Gretchen arrives, distraught that her mother has disappeared. Realizing that only hours remain before Frank's prophesied end of the world, Donnie takes Gretchen and two friends to seek Roberta Sparrow at her house. They are attacked by two school bullies, Seth (Alex Greenwald) and Ricky (Seth Rogen), who are attempting to rob Sparrow's house, and the fight spills into the street. An oncoming Pontiac Trans Am car swerves to avoid Sparrow, who went for her daily walk to check her mailbox, but runs over Gretchen instead, killing her. The driver turns out to be Frank Anderson (James Duval) (a random school kid), wearing the same rabbit costume as the Frank of Donnie's visions. Donnie shoots him in his eye with his father's gun.

As a vortex forms in dark clouds above his house, Donnie drives into the hills and watches the storm as an airplane descends from above. The plane, carrying Rose and the dance troupe, is wrenched violently as one of its engines detaches and falls into the vortex. Events of the previous 28 days recapitulate in reverse order and action, until Donnie finds himself in bed back in the early hours of October 2. As he lies in his bed, waiting and laughing, the jet engine crashes through his room, killing him. Others with whom Donnie had interacted in the 28 days awaken, some looking disturbed. Gretchen rides by Donnie's house and learns of his death from a neighborhood boy, David, but says she did not know him. Gretchen and Rose exchange a glance and wave as if they know one another but cannot remember from where.