Changes from the original in the Director's Cut:
- 2 mins: As Donnie Rides into town the music has changed from Echo and the Bunnymen's The Killing Moon to INXS's Never Tear Us Apart.
- 6 mins: Before Donnie's mum enters his room after dinner she has a short discussion with Elizabeth, asking how she knew Donnie has stopped taking his medication.
- 9 mins: As Donnie is awakened by Frank's voice we see a close up of his eye opening with Frank reflected in his iris. Also the sequence as he leaves the house is extended slightly.
- 16 mins: As Donnie, Samantha and Elizabeth sit in the hotel room Samantha tries to think of ways to make money from the accident, and Donnie tells her when she falls asleep he's going to "fart in your face."
- 17 mins: As Donnie's parents discuss Frankie Feedler the scene is slightly extended, Donnie's dad thinks someone was watching over him.
- 23 mins: As Gretchen Ross makes her first appearance in the classroom more reactions can be heard from the classmates.
- 24 mins: As Donnie and his dad drive, just before nearly hitting Grandma Death, they flick back and forth between radio stations, Donnie wins and music now plays throughout the scene.
- 28 mins: Frank's voice can now be heard during the Cunning Visions video, telling Donnie to watch closely.
- 29 mins: Another shot of Donnie's eye opening as Frank awakens him before he floods the school, water is seen reflected in his eye this time.
- 30 mins: Whilst waiting at the bus stop, before they hear school is cancelled, Donnie steals Samantha's poem and torments her. Donnie's friends also have another opportunity to bully Sharita Chen, calling her Porky Pig, and saying "I hope you get molested."
- 31 mins: More rumors fly around as to why school is closed.
- 33 mins: As Donnie walks home with Gretchen he mentions how he wants to be able to "change things."
- 37 mins: As the police check the student's handwriting we see Donnie looking nervous, and Karen Pomeroy noticing it. This also fixes the continuity as all the previous names on the list are called before Donnie.
- 41 mins: Newscast. Before the emergency PTA meeting Mrs. Farmer and Karen Pomeroy exchange words about Mrs. Farmer's intentions to get The Destructors banned.
- 44 mins: Donnie's English class have a poetry day, where Donnie reads a poem about himself and Frank. "A storm is coming, Frank says a storm that will swallow the children and I will deliver them from the kingdom of pain I will deliver the children back the their doorsteps And send the monsters back to the underground I'll send them back to a place where no-one else can see them Except for me Because I am Donnie Darko" Karen Pomeroy then asks him who Frank is, Donnie tells her he's a six foot bunny rabbit, and everyone laughs at him.
- 53 mins: We see the first of the excerpts from The Philosophy of Time Travel, concerning the tangent universe.
- 59 mins: We see Donnie waiting for the school bus a plane flies overhead and everyone looks up nervously, then the second excerpt from The Philosophy of Time Travel appears, Chapter 2, Water and Metal. Behind this transition there is a short new scene where Donnie sits down next to Gretchen and she asks him why he has blood on his neck.
- 61 mins: We see Donnie's parents out for dinner, discussing what they should do about disciplining him after the incident with Mrs. Farmer. Their opinions are wildly different, and they joke about getting divorced.
- 62 mins: Whilst the parents are out to dinner we see that Donnie and Elizabeth have been sitting at home carving the pumpkins seen later in the film.
- 64 mins: Another shot of Donnie's eye opening, along with footage of waves breaking on a beach.
- 65 mins: We see Donnie and Gretchen in an arcade, the scene is overlaid by chapter 7 from the book, The Manipulated Living.
- 66 mins: As Donnie watches Jim Cunningham's seminar at the school his perception changes, he sees things speeded up, and mentions to Gretchen that he is travelling through time. The seminar now goes on longer, with extra scenes before Donnie steps up to the mic.
- 71 mins: Donnie and Gretchen go to visit Roberta Sparrow, there is nobody home but Donnie checks her mailbox and is inspired to write to her. This scene is overlaid with chapter 4 from the book, the Artifact of the Living.
- 74 mins: Karen Pomeroy tells the class they are no longer allowed to study The Destructors, and that their new book will be Watership Down, however if any student wants a copy of Graham Greene's book someone has put 20 copies aside at the Sarasota Mall.
- 75 mins: Another overlay from The Philosophy of Time Travel, this time chapter 6, the Living Receiver.
- 81 mins: Another eye opening shot, this time with flames reflected in it.
- 87 mins: Another overlay, chapter 10, the Manipulated Dead.
- 88 mins: Donnie returns home the morning after the fire and talks to his dad in the garden. His dad tells him that no matter how crazy he thinks he is, he should always say what's on his mind.
- 90 mins: As we see Jim Cunningham arrested on TV the voiceover on the TV is slightly different.
- 91 mins: Karen Pomeroy's firing is slightly shortened.
- 92 mins: Karen gives one of her last classes, after the students watch a section of Watership Down they discuss Fiver (the rabbit)'s visions, and how trusting those visions of the end of the world would save the warren. Gretchen and Donnie argue in the class about the meaning of them. Donnie doesn't see the point of crying over a dead rabbit, Gretchen tells Donnie he missed the point, and Karen Pomeroy tells the class that the Deus Ex Machina is what saved the rabbits.
- 97 mins: Donnie says goodbye to his mom in the street as she goes to LA with Sparkle Motion.
- 98 mins: As Karen clears out her desk, her talk with Donnie is different, she suggests on a Friday night Donnie should be out scaring old people.
- 103 mins: Donnie talks with his doctor about his belief in God, and she tells him he can stop taking his medication as they are placebos.
- 106 mins: There is an overlay of Chapter 9, the Ensurance Trap.
- 110 mins: As Donnie walks around the party, observing people's channels, there is another montage of his eye, as if he were putting all the clues together that lead him to thinking he should go to Grandma Death's house.
- 114 mins: As Donnie is pinned down with the knife to his throat outside Grandma Death's house, it is now very clear he is saying Deus Ex Machina.
- 116 mins: Roberta Sparrow tells Donnie a storm is coming, and that he must hurry.
- 118 mins: We see a montage of things reflected in Donnie's eye as Frank counts down to the end of the world.
- 120 mins: Another montage as we see the universe collapsing and rewinding as Donnie travels back through time.
- 123 mins: The final overlay is of chapter 12, Dreams, which explains why everyone seems to be having a sleepless night as Mad World plays.
A director's cut of the film has been released. This new cut includes additional scenes, some changes to the soundtrack, a much improved sound mix. Also, pages from the Philosophy of Time Travel, previously viewable only as a DVD extra or on the website, have been inserted between scenes. The result is a movie that tells a much more coherent story.
In the original version, when Donnie first begins to witness the liquid spear coming out of his chest, the spear moves across the room, turns back toward him and forms a large sort-of finger that beckons him to follow. In the Director's cut, the spear does not beckon him. He simply follows. Also the soundtrack in this scene has changed. Previously, we could hear the TV advertising the Middlesex Halloween Carnival. This has been replaced with sound effects now associated with any of the oddities of the tangent universe. In the Director's Cut there is also the audio for a commercial for "Who's the Boss?" starring Tony Danza inserted prior to the Halloween Carnival add.
In the Director's Cut, Gretchen is now heard saying "Fuck 'em!" while flipping the bird at Seth and his friend after Donnie warns her about them.
In the Director's Cut, the voice saying "Get off the stage, Cherita!" and "You suck!" (presumably said by Ronald Fisher) are no longer heard after Cherita is done with her dance. Also gone is the catcall right before this. However, added to the scene was more raucous applause instead of the nervous applause from the original version.
The director's cut features many small changes with the sound, when compared to the original:
- Some scenes have different or no music.
- Some scenes have added sound effects.
- Sometimes the music is quieter than it was in the original, allowing us to hear the people talking better
- Some speech is either added/removed
- There is now an "electronic buzzing" sound whenever Frank appears
Also, the line from Frank in the cinema, "I am so sorry", seems to be missing from the director's cut.