Martin Harris (Liam Neeson) and his wife, Liz (January Jones), arrive in Berlin for a biotechnology conference where he is to give a paper. When they arrive at their hotel, also the site of the conference, Martin realizes he left his briefcase with their passports at the airport. While Liz checks in, he takes a cab to retrieve the briefcase. When a truck's cargo crashes into the road, the cab veers into the river. The cab driver, Gina (Diane Kruger), rescues him but disappears into the crowd when authorities arrive.
Martin is in a coma for four days. When he revives, his memory is shaky. When he sees a television news report about the biotechnology conference, he remembers that he is supposed to be there. He checks himself out of the hospital and goes to the hotel. He sees Liz at a reception and goes to embrace her. But she claims not to know him and introduces everyone to her husband, who claims to be Martin Harris (Aidan Quinn).
Martin wanders the streets of Berlin. He tracks down Gina, an illegal immigrant working several jobs. She doesn't want to help him because she risks deportation. Martin goes to meet Professor Bressler (Sebastian Koch), a German bioscientist with whom he had had phone calls about their plans to revolutionize food production. But when he arrives, Martin B is already there. After an argument, Martin is escorted out by police. He checks himself back into the hospital for more tests. One of the nurses gives him the name of a private detective. After one of the tests, a hit man kills the nurse and tries to abscond with Martin, but Martin disappears into the crowded emergency room and escapes.
Martin goes to see the private detective, Ernst Jurgen (Bruno Ganz), a former Stasi officer. Jurgen believes Martin's story, and tells him to track down Gina again. He finds her and asks for a place to stay for the night, giving her a watch that Liz gave him on their anniversary. As he takes a shower, the hit man bursts in. Gina kills him with his own poison. As they escape in a borrowed cab, they are pursued by a second hit man. They elude him by hiding in a discotheque.
Martin and Gina meet with Jurgen. He has a friend at the airport searching security camera footage for Martin, and has contacted Martin's colleague, Rodney Cole, who Martin is certain can help. Martin follows Liz to a photography exhibition. At first she pretends not to know him but pulls him aside to tell him that she is being forced to betray him and that she still loves him and will wait for him at the airport. When Martin B and the second hit man appear, Martin is barely able to escape with Gina.
Rodney Cole (Frank Langella) arrives at Jurgen's office. Realizing who Cole really is, Jurgen takes cyanide rather than reveal what he knows. Martin and Gina retrieve the briefcase with the passports and thousands of euro in cash. Gina leaves Martin to wait at the airport. Cole arrives and takes Martin to a black van where he is tasered by the second hit man. Gina sees this and follows the black van in a stolen cab. Cole and the hit man take Martin to the top level of a deserted parking garage. Cole explains to Martin that he is really a government assassin using "Martin Harris" as a cover. When Martin woke up from the post-accident coma, he believed his cover story was the truth, so Martin B was called in to finish the mission. Before the second hit man can kill Martin, Gina crushes him between the van and cab; the impact sends the van, with Cole in it, crashing to the ground below.
Martin now remembers everything. Several months earlier he and Liz had gone to the hotel to plant a bomb. It would be used to kill Bressler in a manner that could be blamed on Muslim extremists opposed to the liberalizing plans of Prince Shada (Miro Hamada), who is also sponsoring the biotechnology conference. He and Gina race to the hotel. There, at a reception for Bressler, Liz copies the files containing information about a new, easily grown form of corn, and arms the bomb. Martin arrives in time and persuades hotel security that a bomb is about to go off. When security evacuates the hotel, Liz goes to disarm the bomb while Martin B follows Bressler in order to kill him. Liz fails and is obliterated in the explosion. Martin and Martin B fight amidst the debris as Gina watches. Martin kills Martin B with a glass shard.
The next day, Bressler and Prince Shada freely give their new corn to the world, in their mutual effort to end world hunger. Using additional fake passports found in his briefcase, Martin and Gina leave Berlin together, as Henry and Claudia Taylor.