Deja Vu, like many other time travel movies, has a complex plot. The key to understanding the plot of this movie is the time-travel explanation given at one point by the female scientist. She explains, in so many words, that when a person travels back in time, a new timeline is created that branches off in a different direction from the original path. The original timeline, from the point of the branch forward, either continues in parallel or ceases to exist altogether. So when Doug goes back, he creates an entirely new branch in time in which the events from the original branch never occurred. From Doug's perspective, everything he's experienced from the branch-point forward gets reset.



Initially, you might assume that after Doug traveled back in time, he was operating in the same timeline he left. You might also assume that the clues he has already found in the future are the ones he himself left after going back. But if he created an entirely new timeline when he traveled back and the original timeline is no longer accessible, then he personally could not have left the clues in the original timeline. So who left them? It must have been another version of himself from an earlier timeline. This earlier Doug must have already gone back in time before the beginning of the movie and left the clues. In other words, it took two attempts to save Claire (Paula Patton) and the ferry. Following is the sequence of events:



(Events Before the Beginning of the Movie)



Timeline #1: Claire gets a call from the terrorist, who wants to buy her SUV. The terrorist kidnaps Claire. He kills her and puts a bomb in her SUV. She does not go back to her apartment and change into a red dress. The terrorist dumps her body in the river and drives the SUV onto the ferry. It explodes. In this timeline, there is no Doug from the future to interfere. There are no clues in Claire's apartment, no fingerprints, no odd answering machine messages, no ambulance at the bait camp. Present-day Doug investigates the bombing, but of course finds no clues from the future. He decides to use the time machine to go back and save Claire.



Timeline #2: Using the time machine, Doug travels back four and one-half days. This breach instantly creates a second branch in time. This new timeline is a fresh start, so to speak, a new chance to prevent the bombing and save Claire. At this point paradoxically, there are two Dougs, present-day Doug and future Doug. Remember that the scientist told Doug that he might be dead when he landed in the hospital and that his other self might come to the morgue and find him dead on the slab. When future Doug arrives in the hospital, present-day Doug is still going about his normal life, unaware that anything unusual is going on. Future Doug manages to survive his trip and steal an ambulance from the hospital. He crashes it into the bait camp. He rescues Claire and leaves clues ("U can save her") and fingerprints at Claire's apartment. He knows that if he fails in his mission, present-day Doug will find the clues. Claire calls the ATF office to find out if Doug is legit. She changes into a red dress. Doug then makes a critical mistake. He leaves Claire at the apartment, thinking that she will be safe. However, the terrorist, who knows where she lives, shows up and kills her. He cuts off her fingers and burns her to get rid of DNA evidence. He puts her in the SUV, drives to the river and dumps her body at 10:42 a.m. He drives the SUV onto the ferry and leaves. Doug tries to find the bomb and defuse it but fails. So in this timeline, he is not able to save Claire or the ferry. Everything so far happens before the start of the movie.



(Events After the Beginning of the Movie)



The ferry blows up at 10:50. It is this explosion that we see at the beginning of the movie. Future Doug is killed, but no one is aware of it because his body is one of the bodies bagged up on the dock, this is proven because Doug hears a phone ringing that he thinks is his but realizes a "similar" ring tone is coming from a corpse, unbeknown to him it is his own. The movie follows present-day Doug as he investigates and finds the clues and the crashed ambulance. If he had not gone back in time previously, there would have been no clues in Claire's apartment, no crashed ambulance and her corpse would not have been wearing the red dress. The scenario would have been like Doug's investigation in timeline #1. Soon after the bombing, Doug returns Claire's call from earlier that morning and leaves a message on her answering machine. When Doug goes to Claire's empty apartment, her cat acts like it knows him because future Doug has just recently been in the apartment trying to save Claire. Present-day Doug uses the time machine to look into the past all the way back into timeline #1, before timeline #2 branched off, that is, before future Doug arrived. When the terrorist is caught, he acts strangely because he just killed future Doug a couple of days ago.



Timeline #3: Present-day Doug decides to use the time machine to go back in time once again. As he is sitting in the time machine, the FBI scientist makes the comment that he looks like he's done this before. Doug answers, "Maybe I have." This is an obvious hint that he (actually an earlier version of himself) has gone back in time before. After Doug's trip back, a third timeline is created. Doug has one more chance to prevent the bombing and save Claire. He crashes the ambulance again and leaves the same clues and fingerprints as before, just in case. But this time, perhaps because of all the clues left by the earlier Doug, he manages to save Claire and avoid getting killed. When he takes Claire back to her apartment, he first tells her to stay there, but in a moment of "déjà vu", he has a feeling that he should take her with him. They go to the ferry and prevent it from blowing up. But future Doug dies, neatly avoiding the question of whether time "twins" meeting each other would cause an anomaly. The present-day Doug in this third timeline gets the girl...end of movie.



To summarize, in the first timeline that we never see, the ferry blows up. In the second timeline, the ferry blows up again, and this is the beginning of the movie. In the third timeline at the end of the movie, the ferry is saved. Edit