Even though the main explanation is consistent and ties the whole movie together there are still a few parts of the movie that are not explained and have to rely on theory. Here are some of those questions with possible explanations and some common mistakes people make.
What Creates The Tangent Universe
Why exactly does a Tangent Universe (TU) occur? Are they a natural phenomenon or are they artificially created. There is one theory that scientists in the future build a machine that somehow causes a rip in time back in the past. Another theory is it could have been caused by Alien involvement.
Quite a common thought is Frank saving Donnie in the beginning is the cause of the TU. Donnie was meant to die and by surviving he altered things which caused the corruption. This is not true though, we are already within the TU when Frank wakes Donnie up. Frank's special powers only work within the TU so he would only be able to wake Donnie after the TU had started.
The same goes for the Artifact not being the cause of the corruption. The jet engine appears several minutes after the TU had started. The Philosophy of Time Travel states that the Artifact is the first sign of evidence that a TU has occurred.
The First Jet Engine
One major question is where does the jet engine in the beginning of the movie come from originally? If it came from the future where exactly and what day did it come from?
A common answer to this question is it's the same engine Donnie sends through the portal from the plane his mother and sister were on. The engine travels through time and lands on Donnie's house. It's exactly the same event as the end of the film only the first time round Donnie survives.
This is extremely unlikely though as the portals are just a gateway between the two Universes. The first engine lands in the Tangent Universe (TU) so if it came through a portal it would have to come from the Primary Universe (PU). The engine Donnie rips of the plane at the end is from the TU and travels through a portal into the PU so there is no way it can be the same event repeating.
If it did come from a future point in the PU once the corruption is fixed by Donnie that future event won't happen now so we will never find out exactly how it occurred.
Another theory is the Tangent Universe is a copy of the Primary Universe but as it's being formed there is a glitch or copying error. This error produces a duplicate engine that is then dumped into Donnie's bedroom. This anomaly makes the TU even more unstable and it must be sent into the PU.
Roberta Sparrow: The Philosophy Of Time Travel
Roberta Sparrow writes the book "The Philosophy Of Time Travel" which helps guide Donnie but how exactly did she know all this information? There are a few plausible explanations for this. It seems like she had a similar experience herself so either she was a Living Receiver or one of the Manipulated Dead in a previous Tangent Universe.
Both options would in theory give her all the information required. If she was a Living Receiver she would obviously have known what to do and the Manipulated Dead have a large understanding of what is happening within a Tangent Universe. It's possible she may have somehow retained some of the information from her experience once the Primary Universe started up again.
Does Donnie Have To Die
This subject is one of the most debated parts of the movie. A lot of people make the mistake of thinking Donnie waking up and cheating death in the beginning is what caused the Tangent Universe (TU) to occur. The assumption is then once the Primary Universe is restored Donnie stays in bed otherwise he risks causing another TU to start and the whole cycle will repeat. This theory is not correct though, Donnie and Frank have nothing to do with the creation of the TU.
We hear about other Living Receivers in The Philosophy of Time Travel who were killed by the Artifact they returned. If we include Donnie then it seems the Living Receiver always dies once the Primary Universe is restored. The question is what would happen if Donnie got out of bed again and survived? The moment we see Donnie laughing in bed at the end the Primary Universe is already restored. If Donnie got out of bed and dodged the second engine after that then in theory nothing would change as the corruption is already fixed.
Another important point is whether Donnie chooses to die. The Donnie we see in bed at the end is not the same Donnie from the last 28 days. How much knowledge he has of what happened in the TU is very questionable and it’s quite unlikely he knows he is about to die.
The question of destiny plays quite a big part here, Donnie was meant to die but Frank saved him. It’s possible he was chosen as the Living Receiver because his life is now expendable; he is going to die anyway. Once back in the real world it's Donnie's destiny to die.
Why does frank tell Donnie why are you wearing that stupid man suit is he referring that he is not a man at all?
I will try to answer some of your questions.
to y2e, Frank saves Donnie, because without him (Donnie) the PU would not have been able to be restored. Donnies purpose is to right the wrong of the universe. Afterwards, when Donnie awakes, Frank no longer has any powers, so he is no longer able to save Donnie.
to Mom, No the mother and little sister do not die in the PU. Reason being, once the PU was restored, the events of the next 28 days would be completely different from the ones we saw in the movie. Donnie being dead prevents Jim Cunninghams house from burning, preventing Ms. Farmer from being able to fly with the girls, assuming they even still make it to LA.
to Csosa430, Roberta was waiting all day every day, because she did not know neither who would be the living reciever, nor when a TU event would occur.
As for the question of dying alone. It is the entire romantic plotline to the movie. Gretchens purpose is to make Donnie feel loved, and therefore not alone. This makes him comfortable with the fact that he has to die to restore the universe.
to MalloryH, the plane with his mother and sister on it was clearly in the TU, THE MAJORITY OF THE FILM IS IN THE TU...
to John, the "liquid" was the vectors that Donnie was discussing with Dr. Monnitoff. The scene where he informs Donnie he can not go on talking about god because he might lose his job.
The idea was this; If the universe was predetermined, then you could break the rules and do what you want, assuming you could see the played out universe. But when Dr. Monnitoff told Donnie that he contradicted himself, Donnie said it could still work assuming that God wanted you to go within his "vector". I do not remember if that was the exact word used, but the idea is pretty much there.
Also, on a side note, I wish that at the end, when Gretchen asks what his name was, She would have said something to the effect of "Sounds like a superhero". That would have made the ending 100x better.
There's still one thing I can't figure out, even with the thorough explanations on this site. When the TU collapses, and we return to October 2, the jet engine still crashes (the one which kills Donnie). We know that when the engine crashed the first time (when Donnie leaves the house), it was an Artifact whose presence signified the start of the TU. As the PoTT explains, the presence of an Artifact defies logical explanation, which is why nobody can figure out how it got there or where it came from.
When we return to the PU, no Artifact should be visible, because an Artifact's presence signifies the existence of a TU. Why, then, does the jet engine nonetheless crash in the PU? I can only conclude one of the following: (1) we are brought back to October 2, and another TU starts, only in this one, Donnie dies and cannot save the world, so when October 30 comes again, the world ends; or (2) the airplane from which the jet engine fell is located, and we simply aren't told about it in the film. I'm leaning toward the second, even though it's less satisfactory, because the website describes events occurring nonetheless after October 30, 1988, like the deaths of Roberta Sparrow and Kenneth Monnitoff.
In addition, I've discovered something that is never discussed in the film commentaries or on any fansite: a calendar from 1988 easily reveals a number of logical incongruities in the film. In one scene, Donnie is seen in school on a date which was a Saturday, and in another, he is seen in a therapy session with Dr. Thurman on a date which was a Sunday. I'd like to take the easy way out and say that Richard Kelly simply didn't research the days of the week on which these dates fell on in 1988. I can't believe this, because Donnie is shown having an accurate calendar on his wall, and the day and date of the newspaper column which outs Jim Cunningham is correct. Even the smallest props in the film cover these details, so why not the overall storyline? Has anyone ever noticed this?
The science teacher gives a clue during his talks with Donnie. In order for time travel, theoretically you would need a large source of energy coupled with an object traveling at the speed of light. If a plane in the PU were to be struck by lightning for example, the amount of energy from the explosion coupled with speed of the lightning strike could potentially create a ripple in reality, opening up a TU. The Artifact, in this case a plane turbine, would be stuck in the TU. Because the Artifact is in the TU it is no longer within the PU. An identical Artifact, from the TU, must be sent through a ripple in reality back into the PU in order to restore the balance of the universe. No object can disappear completely and no object can be duplicated. These two events would cause a black hole to form destroying reality.
To correct itself the universe creates someone that can patch up the universe. For this event Donnie is the one that can fix things. There is no apparent reason for why Donnie was selected by the universe. It would appear that the turbine simply landed in his room by chance.
The portal we see at the end of the movie, in which Donnie throws the new turbine, would be a reflection of the portal that had been created by the original event in the PU.
I really don't get one thing. Why did the rabbit save Donnie in the beginning? If he would just laid in his bef, he would have died, just like hey should've.
His mom and sister were never on the plane in PU, only in the TU. Once Donnie set things right in the PU by sending the jet engine through the portal, the past 28 days were erased. Therefore the mom and sister were never on the plane, time goes back to the moment in the PU when Frank called Donnie out of bed. They were all asleep in bed.
I think Donnie HAS to die in the PU because, just like the Manipulated Dead, his superhuman powers originate from him being dead in one universe but alive in the other. Frank and Gretchen die in the TU, but not in the PU, so they have the most profound Manipulated Actions. Donnie ALONE dies in the PU but not the TU, which grants him the powers of the Living Receiver: seeing the future, telekinesis, superhuman strength. If he didn't "allow" himself to die, he wouldn't have the powers in the TU to telekinetically send the engine through the wormhole-of-impending-doom and fix everything. You have to remember that all of this is predicated on the "concept" that the 4th dimension (time) gets "broken" or f's up from time-to-time. This means there is no Cause-THEN-Effect, timelines goes out the window. Of course, none of this will make 100% sense because it is Sci-Fi after all :P
Ha-Mo, it's possible that the plane's pilot was a Manipulated Living, and subconsciously led him to the exact spot he needed to be to drop that plane on the CHOSEN ONE: Donnie.
Does the mom and lil sister die?
QUESTION! Why was the old lady waiting for mail? I know she was waiting for donnies letter, but couldn't she have just talked to him? he lives right there...
ANOTHER QUESTION! What was the significance of the lady's quote, "Every creature on earth dies alone."???
The short part where it shows Donnie's mom and his little sister Samantha on the plane doesn't seem to be that emphasized. If the engine that fell in Donnie's room, that he ripped the engine off of, in the end in the PU came from that same plane, then wouldn't that mean his mom and sister would've died or possibly gotten injured from that accident? It never says anything about the actual plane the engine came from, yet in that short scene it just shows his mom and sister on that plane. And then, when the engine falls in Donnie's room it shows his mom waking up at the house in her bedroom? Was the plane his mom and sister were on in the TU or PU? Cause of it were in that PU then that would mean his mom and sister wouldn't have even been at the house at the time the engine fell through the roof. Very interesting.