I have the basic understanding that the entire plot to Donnie Darko revolves around time traveling. As far as the ending is conceded, you may have various interpretations of what actually happened. The Director's Cut does dive into the book on time travel a bit but leaves me wanting a better explanation for what we see on screen. So what are the common theories to Donnie being dead or alive in both prior to the first plane engine crash and the second one seen in the final scene? Is that enough to understand the overall timeline (which is very complex and super confusing).
I think it is a mistake to take the events of Donnie Darko literally, or to look for a logically consistent timeline or timelines.
There is a key extra scene on the DVD, in which Donnie is having a conversation with his father and says, "Dad, I'm crazy." Not sure why this was omitted, but it strongly supports the interpretation that the film shows Donnie losing his mind -- as do all the included scenes involving Donnie's psychiatrist, who recognizes what is happening to Donnie.
Indeed, Donnie's experiences in the movie are textbook symptoms of schizophrenia:
-he feels increasingly separated from family, friends, and peers
-he thinks he can see into the future
-his fantasies -- like outing Patrick Swayze's criminal character, or (ahem) saving the universe -- put him in white-knight, savior-type roles
-to him, the logic of the whole thing makes perfect sense, but to anyone else, it is beyond comprehension
Personally, I think part of the genius of Donnie Darko is that -- just like many real-life schizophrenics' hallucinations -- Donnie's fantasy almost starts to make sense if you strain to understand. But ultimately it only really makes sense to Donnie.
There is a total of 2 timelines that we observe in Donnie Darko.
The primary timeline, is the one we see at the beginning of the film, starting from Donnie waking up in a random location, biking his way back home. We continue seeing this timeline until the night he first sees Frank.
It is in the next few hours after this encounter, that the Tangent Universe is created. This is due to Donnie not being in his bed when the jet engine hits his room. He is meant to die in this encounter due to some unknown rules of the Universe, better explained in the book. (I think even the book mentions that this can occur for unknown reasons).
During the rest of the film, we are presented the Tangent Universe until the end of the film, when the World is about to end. Donnie summons a portal to lead both himself, and the jet engine back into the Primary Universe, the same night that he left his bed to see Frank for the first time.
It is when we see him start crawling into his bed that we are back in the Primary Universe until the end of the film.
I tried explaining it here:
Hope this helps