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The Bourne Trilogy is composed of The Bourne Identity, The Bourne Supremacy, and The Bourne Ultimatum. While originally books by Robert Ludlum, the first book was adapted into a miniseries in 1988, which was reasonably true to the book, and the three were made into a trilogy of movies, directed by Doug Liman (Identity) and Paul Greengrass (Supremacy and Ultimatum). All that the movies have in common with the books are the titles, the bare-bones of the plots, and some character names (and even then, not really).
Calling it a 'trilogy' is somewhat of a misnomer, because the fandom encompasses nine books, three movies, an upcoming video game, and a miniseries.
The books are completely different in almost every aspect from the movies. Much more focus is put on twisty, convoluted plots that seem like someone stuck eight different books into a blender.
There are six additional books by Eric Van Lustbader, but they are bad because, like a bad fanfic, they disregard all previously important canon characters except for Bourne. In the interest of completion, however, they will be detailed.
The Bourne Identity
A man is fished out of the Mediterranean and brought to Ile de Port Noir, where Dr. Geoffrey Washburn tends to his wounds, including a bullet in his skull, and lets the neighborhood children watch him have multilingual nightmares. Washburn finds a dot of microfilm that was surgically implanted in his patient's hip, which has the name of a Swiss bank and an account number on it. The patient wakes up to discover that he has amnesia, which is Most Distressing. Washburn sends him to Zurich, and the amnesiac does a number of shiny ninja things to get there. Once the amnesiac arrives in Zurich, he goes to the first hotel that catches his fragmented memory, and the clerk recognizes him. The amnesiac pretends to have a sprained hand, and the clerk fills out the registration for him – J. Bourne.
With at least a surname now, Bourne heads off to the Gemeinschaft Bank, where his account is. Once he opens the account, he discovers $5 million in it, and immediately wires $1 million to Washburn as a sort of 'thank-you', then wires the remainder to Paris. He also discovers an envelope from the mysterious and Very Important Treadstone Seventy-one corporation, along with documents naming him as Jason Charles Bourne. Upon leaving the bank, it is discovered that the bank was having him watched all along, and this was actually just a Big Scaly Trap. There is a shoot-out, and Bourne flees. A man with gold-rimmed glasses (like Noah Bennet in Heroes; this man is hereafter known as GRG) is noticed and is Very Important later on because he's trying to kill Bourne.
Back at the hotel, Bourne meets a woman, who is identified through observation and eavesdropping as Dr. Marie St. Jacques, auburn-haired Canadian economist and the designated Love Interest. To try and evade his pursuers, who would be looking for a man alone, he effectively kidnaps St. Jacques and escapes. There is an epic chase which leads them to a restaurant, which then in turn leads them to this other random guy, who is apparently a contact of Bourne's. He shoots Bourne after dropping some tantalizing hints about 'Carlos' before he is killed himself. Bourne tells Marie to drive them to a boarding house on the Steppdeckstrasse, and Marie, realizing a good chance when she sees one, gets the hell out of there, leaving Bourne to bleed out. She goes to the 'police'... who are led by GRG. So Marie has just fallen into a scaly trap of her own.
Bourne passes out at the boarding house, only awakening when GRG's cronies have invaded. He then proceeds to pwn the crap out of them, stealing their car keys and trying to escape. He is caught by GRG, who alludes to Bourne's being a killer, orders Marie's death, and tries to break Bourne's fingers. Bourne ninjas out of the scaly trap and finds Marie, who is about to be raped by the man who is going to kill her. He tries to kill the would-be rapist, who runs off, but not before wounding Bourne. Marie, now looking upon the man who had initially kidnapped her as her savior, piles him into the car and drives off to get him patched up. When he wakes up, there is mild exposition, and he tells her his life story as he knows it. There is much memory angst as they both heal emotionally. And then, after sufficient time has passed for Marie to recover from being almost raped, they have sex. This is okay because they are soulmates.
Marie then tells Bourne that this 'Carlos' is none other than Carlos the Jackal, internationally renowned assassin of Europe who operates out of Paris. Naturally, they go to Paris. Marie sends a telegraph to her boss in Ottawa to see if he can find out anything about the mysterious Treadstone Seventy-one. Marie and Bourne work together and discover that the Gemeinschaft Bank's liason to France is crooked and, unsurprisingly, wants to see Bourne dead. After some coercion, Bourne discovers that Treadstone Seventy-one is located in New York. It is then discovered that Marie's boss has been killed for prying, shot in the throat – the Jackal's preferred method of assassination. Then Bourne goes to hang out in a dress shop to find out some things about Carlos the Jackal. (Seriously.) Bourne then does some ninja sneaking, gets information out of the store's owner, a crony of Carlos's, and is noticed by someone who works at the store, a former colleague who identifies him as 'Cain'.
This is Very Important, because the scene transitions to the Pentagon, where many people are talking ominously about 'Cain'. It is revealed that Cain is a high-level CIA operative of some sort, who kills people, and has been hunting for Carlos the Jackal. More exposition occurs, in which it is also revealed that Bourne used to be in a secret unit called 'Medusa' full of vicious bastards during the Vietnam War. It is implied that Cain and Carlos are going to find each other and fight to the death. Jason Bourne's name is on the official Medusa casualty list, so the plot thickens into cement. Back in Paris, the grey-haired switchboard operator exposits to the owner of the dress shop about what he knows about Cain, alias Bourne, alias Delta of Medusa.
Meanwhile, Bourne is being exposited to about Medusa by Jacqueline Lavier, who works at the dress shop, and suffering from some gnarly flashbacks. He makes his way back to the hotel and prepares a way to get Marie on a plane to Ottawa so she's not caught up in his web of destruction. Unfortunately, it's too late; Marie's face has already been plastered all over the papers in connection with the people Bourne killed in Zurich. This is a Bad Thing. They read the article after Marie's calmed down, and realize that someone is trying to send them a message.
Back in Manhattan, everyone in the fortress that is Treadstone is killed because of inept government bureaucrats, and Bourne's fingerprints are planted at the scene to convince everyone that he's turned evil. The remaining Treadstone people, including one Alexander Conklin, are convinced that Bourne snapped and that he must die. It is revealed that one of the dead people at Treadstone HQ was Bourne's brother, so we find out that Bourne's real surname is Webb. Back in France, Bourne has just told Marie everything that he remembers, which isn't much. They call a number that Bourne was able to get out of Lavier, which connects them to the home of a respected French general. And the plot thickens some more.
Bourne sneaks around and meets up with General Villiers, who swears that he's not in league with the Jackal because the Jackal killed his son. It is discovered that Villiers' young wife is the contact (and, for added squick, she has been the Jackal's lover since she was fourteen). Lavier is killed, and once Bourne calls in, trying to contact the Treadstone administrators, Conklin hops the next plane to Paris. There is a graveyard confrontation that is made of much epic. Bourne tries to tell Conklin that he's lost his memory, but Conklin will have none of it.
The Bourne Supremacy
Marie is kidnapped by rogue elements within the American government who are trying to make it seem like the Jackal is responsible. Bourne gets pissed, recruits his ex-handler and his psychiatrist, and storms Hong Kong in an Epic Quest for Marie.
There's also a lovely little bit of comic relief involving a train station, a stuffed panda, a porn magazine, and a guy in drag. Seriously.
The Bourne Ultimatum
The Bourne Legacy
The Bourne Betrayal
Among other things, the movies are responsible for turning Matt Damon into an action star. This is recognized by many as a good thing, but the screaming fangirls that inevitably follow Matt Damon are a bad thing. The movies are also renowned for their fight scenes, which run at Ludicrous Speed, and generally involve Matt Damon kicking the crap out of someone with a household object, such as a pen, book, or magazine.
A point of contention is the camerawork of the second and third movies, something that has almost become a signature of the series. The average length of a shot is just under two seconds, something which makes the movies either more hardcore or more headache-inducing, depending on who you ask.
The Bourne Identity
A man is found floating in the Mediterranean with two bullets in his back. It is assumed that he is dead, but he moves, so he's just unconscious and in shock. The fishing boat's medic digs the bullets out of him, as well as a strange little laserpointery gadget that's been implanted under the skin near his hip. When aimed at a flat surface, it shows the name of a bank in Zurich and its account number. When the medic turns back to the table, the (now wetsuitless) man has disappeared, only to freak out and attack the medic shortly after. Once the man's name is asked for, he reveals that he doesn't know, and keels over.
Two weeks later, the boat is putting into shore. The man still does not know his name, but heads to Zurich with meager funds scraped together by the crew of the fishing boat. Since he is now completely broke, he and his moth-eaten sweater decide to sleep on a park bench for the night. Two Swiss policeman-officers will have none of it, however, and decide to arrest him. The man tries to explain that he doesn't have any papers in the German that he inexplicably knows, but the policeman-officers still are having none of it. One of them pokes him with the baton, and suddenly all hell breaks loose. In approximately five seconds the man has disabled both policeman-officers and stolen a gun from them. Then he freaks out, takes the gun apart, drops it in the snow, and buggers off.
Morning. Matt Damon is looking woobie and pathetic because he has spent the night freezing half to death outside the bank. He goes in, writes down the account number, and is taken to a shiny and futuristic fingerprint scanner, which verifies that yes, the account is his. He goes into the privacy cubicle and opens the little safety deposit box. He finds contacts, money, and a passport that identifies him as Jason Bourne, who lives in Paris. Hence, you know, the title. Curiously, he takes out the bottom of the box, which is false, and definitely does not like what he sees. There are several passports, each with his picture, scads of phat cash, and two guns. Naturally, he kind of freaks out again and empties everything into the bank-provided backpack, except for the two guns.
The Bourne Supremacy
Two years after the events in The Bourne Identity, Bourne and his girlfriend, Marie Kreutz, are living in Goa, India. Bourne is beginning to recover some of his memories, and he is troubled by disjointed flashbacks of an assassination he carried out in a Berlin hotel. Meanwhile, in Berlin, a CIA officer under Deputy Director Pamela Landy is trading $3 million for the 'Neski Files', documents about the theft of $20 million from the CIA seven years earlier. During the exchange, an assassin named Kirill plants Bourne's fingerprint on a bomb in the building's basement, kills the agent and the source, and steals the files and money, which he gives to Russian oil magnate Yuri Gretkov. Kirill travels to Goa to kill Bourne, but Bourne flees with Marie. As Bourne and Marie are driving away, Kirill fires a sniper rifle at the car and it veers off a bridge into a river. Kirill leaves, believing that he killed Bourne. Bourne manages to swim away undetected, leaving Marie dead in the river. Bourne travels to Italy to learn why he is again being targeted.
After Landy's team finds the planted fingerprint and determines that it is linked to the CIA's secret Treadstone project, Landy flies to CIA headquarters in Langley, Virginia to find out more information. In Virginia, she learns that it is Bourne's fingerprint, but CIA chief Ward Abbott claims he does not know Bourne's whereabouts. Landy tells Abbott that the CIA agent who is believed to have stolen the $20 million was named in the stolen files. A Russian politician, Vladimir Neski, was going to identify the thief, but before he could do so, he was murdered by his wife in a Berlin hotel, who then committed suicide. Landy believes Bourne killed the CIA officer and source in Berlin, so Abbott and Landy set out to capture him.
When Bourne arrives in Naples, Italy, he is detained by an Italian Carabinieri officer and a CIA interrogator, but Bourne incapacitates the two men and, after copying the agent's SIM card on his own cell phone, escapes. This allows Bourne to listen in on a call from Landy; he learns her name and phone number, and finds out that he is suspected in the recent killings in Berlin. He steals a car and heads to Munich, where he interrogates another Treadstone agent, who tells him that the project was shut down following Conklin's death. Landy and Abbott intercept and debrief Nicky Parsons, Treadstone's handler in Paris. Bourne arranges to meet Nicky, whom he interrogates. He learns that Abbott was the head of Treadstone, not Conklin. Upon hearing their conversation over Nicky's transmitter, Landy begins to believe that Bourne is being framed. When Abbott's young associate Danny Zorn tells Abbott that he thinks Bourne was framed, Abbott stabs him. Bourne goes back to the Brecker Hotel in Berlin and remembers more about the Neski mission: he was sent to kill Neski on Conklin's orders; and when Neski's wife unexpectedly showed up, he shot both of them and made it look like a murder-suicide. Bourne then learns that Abbott and Gretkov stole the money, and that Abbott had ordered Kirill to kill Bourne, Neski's murder, the murder of the agents by Kirill, and the planted fingerprint.
Out of respect for Marie's belief in non-violence, Bourne spares Abbott's life. After Zorn's body is discovered, Landy confronts Abbott, who commits suicide. Landy later receives the tape Bourne recorded which implicates Abbott in the conspiracy. Bourne travels to Moscow, where he is shot and wounded by Kirill. After an extended car chase, Kirill is killed in a crash. Gretkov is arrested by Russian police after Landy provides them with the evidence she got from Bourne. Bourne goes to the apartment of Vladimir Neski's daughter so she won't have to live thinking her mother killed her father. He admits that he killed them both on a mission gone wrong, and apologizes. The final scene jumps to New York City, where Bourne contacts Landy to ask why the CIA is still looking for him. After Landy thanks Bourne for supplying the tape, which the CIA has used to settle matters concerning his frame-up, she tells Bourne his real name and birth date. Bourne declines Landy's offer to come back to the CIA offices in person, and he fades into a crowded street scene.
The Bourne Ultimatum
In the books, Marie St. Jacques-Webb is actually married to David Webb/Jason Bourne after the events of Identity. She is also more of a Kidnap Target, and has two children by Webb/Bourne, Jamie and Alison. In the movies, Marie Helena Kreutz is a German drifter who provides Bourne with a ride to Paris, falls in love with him, and is from then on inextricably caught up in the web of deceit that is Treadstone. She is killed at the beginning of Supremacy by a bullet meant for Bourne.
The character of Conklin is drastically different in each 'verse. In the books, Alexander Conklin is an alcoholic, secretly-Russian retired CIA operative, the mastermind of Treadstone Seventy-one and Bourne's adversary/BFF. He also survives throughout the books (not counting the Lustbader additions). In the movies, Alexander Conklin is more of a jerkface, still works for the CIA, and is killed by Manheim, another Treadstone operative at the end of Identity.
Chatvert is going to probably be filling this out all by herself. She's totally fine with that, and actually prefers it, because she is a rabid Bourne fangirl.