Andrew Largeman wakes up from a bizarre nightmare in which he is on a crashing plane to a telephone message from his father, telling Andrew that he needs to return home because his mother has just died.
Andrew leaves Los Angeles and returns home to the state of New Jersey to attend his mother's funeral. He recognizes the gravediggers as old friends, and they invite him to a party that night. He takes ecstasy (after refusing cocaine) at the party, but remains detached, and is also impressed by the abundant usage of drugs; indeed, this is the last time he's seen taking any drugs. At home, Andrew had his father book a doctor's appointment for headaches he's been having. During the scene, the father tells a lie but takes it back, and says he does not know why he lied.
The morning after the party, Andrew proceeds to his doctor's appointment, meeting in the waiting room a girl named Sam, a pathological liar. She will later explain that most times she does not know why she lies, it's like a tic; but still one can trust her to admit her lies. During the scene, she tells him to listen to her music, saying it will change his life, and he does listen and appreciate the song. In Andrew's meeting with his doctor, it's revealed that Andrew has been on lithium, as well as other mood stabilizers and anti-depressants, for his entire adult life, but has stopped taking them. He also says that his father, who is also his psychiatrist, put him on the medications in the first place. Andrew finds Sam outside of the office, eventually offering her a ride home. Sam invites him to her house, and he meets her mother. After returning home, Andrew's father confronts him, who is insistent that they have a talk before Andrew leaves town.
Right after, we see Andrew staring at Mark while he robs a tomb, while another Andrew's friend states that the town is "so messed up" because of drug usage, even if he's not exempt from it. This usage is also depicted directly in a number of scenes throughout the movie.
Andrew then returns to Sam's house, and the two spend the rest of the day together joining his friends later. Andrew tells her that, when he was nine years old, he pushed his mother, resulting in an accident that left her a paraplegic; he says that he believes his father blames him for his wife's paralysis, and put him on his medications to "protect him" from the anger he supposedly harbors. Sam listens non-judgmentally, and Andrew subsequently expresses his interest in her.
The next day, one of Andrew's friends, Mark, tells Andrew that he needs help "tracking down" a going-away present for him. Sam, Andrew, and Mark spend the day tracking the present down, ending in a quarry in Newark where Mark talks to Albert and his wife, a couple who've been employed to watch the area, who also do modest antique jewelry sales. They then discuss the reasons for which Albert and his wife chose to live there. The house is described by Albert as "his private ark", a possible reference to the working title of the movie, "Large's Ark". Also, living there and exploring the abyss which was found in the quarry is described as "doing something that's completely unique, that's never been done before", a direct quote from earlier Sam's speech; but finally, Albert explains that what actually matters is just his family, and the camera shows right after the listening Sam and Andrew. A few moments later, the two of them kiss each other for the first time, after shouting at the infinite abyss for some reason not directly explained in the movie, left to the watcher to interpret.
When they look at the gift, it turns out to be Andrew's mother's favorite pendant, that Mark had taken away from her grave and probably sold. Afterward, Andrew approaches his father for the talk the father had suggested, in which he says he was not to blame for his mother's accident and that, from now on, he will live his life without medication. He nevertheless forgives his father, and says he wants to build a better relationship with him.
The morning after, Andrew says his goodbyes to Sam at the airport, acknowledging that she did change his life, and leaves for his plane that will take him back to his life in Los Angeles, to fix his problems before continue the relationship. We later see Sam desperately crying just before Andrew unexpectedly returns, telling Sam that he doesn't want to waste any more of his life "without her in it."