The movie starts with John Smith (Brad Pitt) and Jane Smith (Angelina Jolie) in marriage counseling. It is apparent that their marriage isn't going to well. The therapist asks how long they have been married, to which John replies "five years", but is corrected by Jane who states it has been six. John corrects himself with "five to six years." (This is kind of a running gag throughout the movie.) The therapist asks them the number of times they've had sex that week, including the weekend, which turns out to be none. Next, the therapist asks them where they met.
Cut to "5 to 6 years ago" in Bogota, Columbia. The place is wrecked by war, and John is alone in a bar drinking. The bartender mentions that someone shot the Barracuda, and police are looking for tourists who are traveling alone. Jane then enters the bar, and is almost captured by the troops when John boldly claims that she is with him. It is seen that John is carrying a hand gun, and Jane has a knife. They go up together into his apartment, where they formally introduce themselves. They kiss, and proceed to get drunk and dance at a local club in the rain. They have sex and go to sleep. The next morning Jane wakes up and John is gone. He soon returns with a newspaper and coffee saying that room service had fled, so he did his best. The kiss some more.
John and Jane are also seen at some kind of fair, and John plays a shooting game to win a prize for Jane. She tries first, and does horrible. John goes next and does alright, winning her a small bear. He claims it is beginners luck. Jane goes again, and hits every target, winning the biggest stuffed bear of them all.
The next scene is John boxing with an unknown person, which talking to his friend Eddie (Vince Vaughn) about how he has been dating Jane for six weeks and that he loves her. We also find out that Eddie is divorced and lives with his mother. Jane is rock climbing with her friend also talking about how much she loves John. Jane thinks that John is in construction, and John thinks that Jane is in some sort of computer-related job. Really, they are both assassins for rival corporations, and both Eddie and Jane's friend are assassins too. John tells Eddie that he is getting married, which they do.
We now see John and Jane in their daily lives, waking up and going to work. It is apparent that everyday is very routine. John is home everyday at exactly 7:00pm, where Jane is waiting with dinner. That night, Jane says she has to go out for awhile, and leaves. Soon after, John leaves also. Jane enters some sort of crime bosses hideout dressed as a dominatrix, and kills him, escaping through the window, using her purse as some sort of grappling hook, and leaves in a taxi as if nothing happened. John drunkenly walks into the back room of a bar to find some guys playing poker, claiming to be looking for the bathroom. He takes a man named Lucky's seat, since he is missing, and plays poker. He's doing fairly well and they're all having a good time, until Lucky shows up. John proceeds to shoot them all and leave, but not before checking out the other players cards. He arrives home precisely at seven.
We see Tank (Adam Brody) walking throughout his office happily, exclaiming that the boss wants to see him. He goes to the elevator that would take him to the boss, but is stopped by his secretary. She says that people have been working there for 25 years, and still hadn't seen the boss. Tank gets his mission orders from the secretary, and it's obvious he isn't excited about them. He gives the camera that the boss is looking through a thumbs up, and leaves.
The next day, both John and Jane (unknown to the other) are given orders to kill Tank, who is under custody and is to be murdered before he is transferred to another person or company. John leaves the house and goes into the tool shed, pulling up a secret hatch that leads to an underground room filled with weapons and supplies. Jane, in the house, pushes buttons on the stove revealing a hidden compartment filled with weapons and supplies. They both leave.
Cut to Arizona. Jane has set up a base in an abandoned building, and has all of her explosives set up, ready to kill Tank. As Tank's convoy is approaching however, Jane spots a dune buggy driving wildly through the desert. The driver unknowingly disables some of the explosives. This ends up compromising Jane's plan. The driver gets out, and it is John. John decides to pee, with his back to Jane. (He doesn't know anyone else is there yet.) Jane is watching him through her binoculars, but can't make out that it is John. John gets out his rocket launcher and starts to walk away from the dune buggy. He notices that he got a little pee on his boots. Jane gets mad however that her plan is ruined, and shoots John. John gets angry and shoots a rocket at her hideout, and it explodes. Jane gets away on a motorbike. John scavenges through the destroyed hideout, and finds a blown up laptop. Both are afraid that their secret identity might be exposed. They are both given 48 hours to discover who the other person is, and kill them, or else.
John takes the laptop to a computer expert who discovers that the computer belongs to Jane.
Jane watches and rewatches the tape of John peeing, and also discovers that it is John.
Disappointment and anger sets in for both of them, and they both know they have to kill each other. John gets home at exactly 7:00pm, and dinner is waiting. He is afraid that the food is poisoned, so is cautious to eat it. Jane is acting very suspiciously. John drops a bottle of wine on purpose, and Jane catches it instinctively. They both know now that the other knows about their identity. John goes to get his gun, and Jane takes off in her car. John tries to stop her, chasing her down the street but it is no good. He accidently fires a bullet in to her windshield and she gets angry. Jane runs him over, and he hangs on to the top of the car. He smashes his way into the backseat, and Jane bails from the car, sending John off a ledge in the car.
John goes to Eddie's all beat up and tells him what happened. Eddie lets John stay there, and advises him to kill her in the morning. Jane is at her office drinking away her sorrows, and trying to convince herself that she didn't love John.
They engage in a few attempts to get the job done, to no avail. It's obvious neither truly wants to kill the other. They meet up at a local restaurant and talk, but bombs set off (set by both John and Jane) and they leave. They are racing back to their home in their cars, and John calls Jane on his car phone. He tells her he still loves her, and that the first time he saw her, the first thing he thought of was Christmas morning, because he didn't know how else to put it. Jane says the first thing she thought was that John was another easy mark, and hangs up. She slams her head back against the seat, because she was clearly lying. They get home, and Jane slams into John's car. He pauses, and then screams, very delayed. (Rather humorous)
They battle it out in a major fight scene taking place in their own home. They are using everything they can find to try to kill each other, including a majority of the guns that were hidden throughout the house, knives, etc. It goes on for some time, and each has taken quite a beating. The house is almost completely ruined. Eventually, they both get each other held up at gun point. John says he can't do it, and lowers his gun. Jane then realizes that she does actually love John, and also lowers her gun. This whole thing has put the spark back in to their marriage, and they end up having sex.
It is early morning, and both have just woken up and are having their breakfast, when we see many assassins sent to kill them. They hide in the cellar where John's weapons and supplies were previously hidden, before Jane took them all. A robot type of machine releases a bomb that bounces down the stairs. John kicks the bomb...right next to a fuel oil tank. They run and dive out of the cellar, just as the entire premises is blown to pieces. All of the assassins are killed. The Smith's take their neighbors mini van and clothes, and goes to see Eddie.
On the way, John is driving and Jane is in the passenger seat. Soon, four or five matching BMWs are shown in pursuit. Jane takes over driving, and John takes out the assassins. Eventually, all of the assassins are taken care of, and John and Jane are talking about all the things in their life that were lies. We find out that Jane's parents died when she was five, and her parents at her wedding were paid actors. We also find out that Jane is Jewish, that John never really liked Jane's cooking, and coincidently, that Jane never cooked once in their marriage, it was all prepared by her corporation.
They meet up with Eddie, who tells them that since they were both given 48 hours to find and kill the other, and the both failed, their companies are out to kill them. He also tells them that they have to find something that the company wants more than them, which is Tank.
Jane goes to her assassin friend from the beginning of the movie as has her locate Tank. Jane is in the van guiding John, and John is crawling through the vents. Jane tells him to wait while she locates the right path to take, but John ignores her and goes his own way. He makes it to Tank, and they both cooperate to get him out from the prison he was held custody at. They take Tank to a motel for interrogation. John is asking him questions, and gives him three options. A) Tank talks, and there is no pain. B) Tank doesn't talk, and John removes his thumbs with pliers, and promises it will hurt, or C) John kills Tank. Tank only responds by asking for a soda. Jane hits him in the face with a phone, and Tank decides to talk. He tells them to look in his back pocket, which they do. There is a picture of the Smith's together. Tank informs them much to their horror that he was not the target, they were. Their corporations found out they were married, and teamed up to make them kill each other. They discover that Tank was just a setup. He was just a bait to lure them into discovering the identities of one another. John goes to beat Tank up, but he tells him to check his belt first. On his belt was a GPS tracking system. John says they have two minutes before they are found. Jane looks out the window and replies "one" as a helicopter is approaching.
They hide in a sewer. Jane has a boat waiting for her, and John has a car drop waiting for him. They both decide that instead of running their whole lives, that they will stay and fight. They hide in a nearby store. They both put on their bullet proof vests, and get all their supplies ready to go. Soon, the store is filled with assassins, and the Smith's fight it out with them all. Jane accidently throws a knife into John's leg, to which he replies that they will talk it about it later. They are both getting shot up, but keep fighting. In a very cool semi-slow motion scene, the Smith's take out all the assassins. They have prevailed.
The movie ends with another session of marriage counseling. This time, their relationship have improved dramatically. John tells the therapist to ask him the sex question again. Jane scolds him, but John just smiles and holds up ten fingers and mouths the word "ten."
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