Joe Miller (Peter Krause) keeps on looking for his daughter Anna (Elle Fanning), helped by Jennifer Bloom (Julianna Margulies), who tells him that wealthy man Karl Kreutzfeld (Kevin Pollak) is crazy and won't really help him. However, Joe feels he's his only hope. He sympathises with him as well because Kreutzfeld's son Isaac (Benjamin Petry) is suffering from leukaemia. Joe wants to find the Prime Object, who he thinks it's the Ocupant (Tim Guinee). He is completely sure that it is real because he's seen his image in the photograph.
Meanwhile, Kreutzfeld is visiting The Sood (Jason Antoon), as he is looking for The Eye, no matter the price. Kreutzfeld buys a book with a map drawn inside, with the instructions to go to a vault where many of the original Objects are. Jennifer and the Sood are checking the copy of a film concerning Arlene Conroy, who made an experiment. She used five different objects and entered Room 9 at Sunshine Motel. Chaos ensued, and she disappeared inside the room forever.
Dr Martin Ruber (Dennis Christopher), is lost in the rocky desert which surrounds the motel. He's got the Photograph, which is one of the Objects, the only one with which you can actually see room 10 and its contents. Margarent Milne (Harriet Sansom Harris), his second-in-comand within the cult called the Legion, is reprimanded as she has lost two objects.
Joe and Karl pay Suzie Kang (Margaret Cho) a lot of money for the information concerning the whereabouts of the Scissors, able to rotate things. Zoraida Figueroa (Remy Ryan Hernandez), a drug pusher, has the Scissors. After a fight which Joe and Karl really need to collaborate, they get the Object. Zoraida is left completely down, as those Scissors were the only things which mattered to her.
Wally Jabrowski (Peter Jacobson) thinks that the Occupant doesn't exist, and that if it ever existed, it must be already dead, as it has been inside the vault for more than 40 years. The vault is inside an Arizona abandoned prison, where John Clark, one of the original Collectors, used to work.
Joe takes the Key, and Karl takes the clock, and they agree to leave the Flask and Joe's gun at Karl's room. Meanwhile, Jennifer realises that Karl wants to repeat Arlene Conroy's experiment. She thinks that it will kill Karl himself and everybody. Within the vault, Karl finds the Eye, but there is nobody inside the wooden box where the Occupant should have been. At that moment, Joe learns that Karl's son is dead, a datum he didn't know. Karl takes a pill, and whoever he remembers, appears beside him. First Isaac and then his thug Anthony (Jason Douglas) appear. Karl leaves with the key, leaving Joe imprisoned. Joe manages to escape with the help of the Objects.
Joe takes Wally's bus ticket, and learns the city of origin of the Occupant. They learn that there was a strange man who appeared all of a sudden, saying that he was married to Mabel Smith (Lois Geary), who had no recollection of him whatsoever. She never married, and kept a photo of herself with the Occupant just married, signed by herself. Detective Lee Bridgewater (April Grace), Joe's ex-colleague, follows Martin and Margaret to hospital. There, Margaret is about to kill the heavily dehydrated man, but he tells her that, when he reunites all Objects, he himself will become god.
Karl takes out his own eye to put on the blue crystal eye. With it, he can make people disappear and presumably, kill them, just leaving their clothes in a heap of dust on the floor. When Jennifer and her friends break into his home to prevent him from doing Conroy's experiment, it's too late, and Karl kills several people.
Joe visits Eddie McCleister (Tim Guinee), who tries to commit suicide, but Objects cannot be destroyed outside the room. Eddie didn't create the Objects: the Event just happened, and he is one more of the Objects. He has this idea to try to get Anna back, and leaves with Joe for the motel room. There, Karl is repeating Arlene Conroy's experiment. He sees his son in the room, but Isaac is afraid of his own father and pulls back. Karl enters the room and they both disappearing, creating a light and sound commotion.
Eddie enters the Room, and Joe follows suit. The Occupant asks him to kill him shooting him with Joe's gun, because he can only be killed inside the room. By the Law of Conservation of Objects, once the original Occupant is dead Joe will take the burden and become an Object.
Finally, Joe does so. He kills Eddie, he becomes and Object and finds Anna. They leave the room. Joe leaves the room with her. He comes back to leave the Key in the Room, closing the door and checking that when he opens the door again he can't see the key. Jennifer, Joe and Anna leave together.
The door opens and we see the key laying there, on the carpeted floor.