Gabe finds his beloved sock monkey, Señor Guapo, sitting at his bedside and telling him, “In dreams begin responsibilities,” in an old man’s voice. In response, Gabe notes that he ended up talking to a parole officer the last time Señor Guapo talked to Gabe. When he realizes that Señor Guapo’s voice has changed, Ian wakes up and suggests they ask the Great Unknown what he thinks. Their hooded roommate is packing and explains that they’re letting him leave Tower Prep. He refuses to show them his face, which he claims is hideous. Ian rips it off and reveals that the Great Unknown is Headmaster.
The next morning, Gabe is at school in his underwear, and CJ has Suki’s head in a box. They go to class but find themselves in the tunnels, facing a yellow elevator door. The elevator begins to open and a bright light shines out, and everyone screams in fear...
And Gabe wakes up from his dream. He turns to Señor Guapo but gets no response. When Ian asks what he was dreaming, Gabe tells him and they realize that they were having the same dream about the yellow elevator doors. They both woke up before the doors opened, and Ian doesn’t believe that it means anything. However, they realize that the Great Unknown is gone, just like in their mutual dream.
In class the next day, Psychology lectures the class about dreams, and asks them to bring out their dream journals per their assignment. Suki describes how in her dream, she’s the most popular girl at Tower Prep. She speaks in the voice of the old man from Gabe’s dream, saying, “In dreams come responsibilities.” Then she finds herself in the tunnel with the others, facing the yellow elevator doors. She kisses Ian and reassures him. Ian explains that he and Gabe had the same dream, but Psychology says that they simply reacted to the same real-life stimuli. Gabe wonders why they’re dreaming about it now, and Psychology says that the elevator doors may represent different things to different people.
The group meets in the observatory, and Ian insists that the dreams are more significant than Psychology is making them out to be. CJ notes that she hasn’t had any dreams since they got their dream journal assignment. Gabe stops toying with a paperweight of an eye and finds an old jazz record. He puts it on and dances with Suki, but when the singer comes on, Gabe and Suki realize it’s the old man’s voice that they heard in their dreams. They’ve never heard the voice before, and Ian figures that they heard it somewhere. If the voice has a real-life counterpart, then he figures so does the elevator door, and they subconsciously noticed it in the tunnels without realizing it.
Down in the tunnels, the group finds the yellow elevator doors, It’s locked with a retina scanner, and Suki identifies it as a much earlier model than the first ones made in the 1980s. Someone comes up in the elevator and they hide, and then watch as a doctor brings out a new student that none of them recognize. They realize they recognize the elevator because it’s how all of them except CJ were brought to Tower Prep. Ian figures that the elevator’s their escape route, but it closes before they can get inside.
The next morning, the new student, Conner Owen, wakes up. His new roommate, Ian, tries to reassure him, but Conner attacks him. Ian fends him off and manages to calm him down by explaining that he went through the same thing. They exchange introductions as Gabe arrives, and Conner admits that he doesn’t remember anything that happened to him. They tell him that he’ll have to wear the school uniform.
In the cafeteria, Conner is surprised to learn that they know his perfect breakfast. Gabe and Ian introduce Conner to Suki and CJ. As CJ studies him, Conner says that they’re all acting normally but he’ll never get used to being a captive. When he goes to get eggs, CJ tells the others that Conner is pretending to be someone he isn’t. When Conner returns, Whisper 119 calls new students to orientation. Ian warns that if Conner misses Orientation, he’ll be taken to Headmaster. Conner throws food at the wall and the Monitors take him away to Headmaster.
Headmaster goes over Conner’s detailed personal records, and Conner notes that most schools don’t have walls to keep the students from escaping. Unaware that Ian is listening in from the tunnels, Conner accuses Headmaster of employing Ian as his goon. Headmaster notes that Conner and Ian are similar, and he’s assigned them as roommates. Conner demands answers and Headmaster learns forward and whispers something in his ear. Apparently satisfied, Conner leaves.
Ian tells the others what he’s learned, but they wonder why Conner is working with Headmaster even in private. As they talk, Ian realizes that Conner mentioned the wall, even though he never went there. He concludes that Conner knows more than he’s saying.
Conner is working on his computer in his room when Gabe and Ian return. He wonders if he can trust them, and they say he can trust them if they can trust him. He shows them a copy of the orientation film that he illicitly downloaded from Whisper It shows Headmaster offering to answer questions, but Conner reverses the sound and reveals a subliminal message: an old man saying “In dreams begin responsibilities.” There’s also a split second image of an elderly one-eyed man against a yellow background. Ian thinks he’s familiar but can’t pace where he’s seen him. They figure the image represents a chance to get the answer to some questions that Headmaster doesn’t want to answer.
Back at the observatory, Ian and Gabe tell Suki and CJ what they found. Ian still thinks that Conner is a plant, but the others suggest that he’s letting his feeling about being call a goon are prejudicing him. Ian notices that the paperweight that Gabe has been playing, with an eye inside of it, belongs to the old man from the video. Ian figures that it’s been there since before he’s been there. CJ figures that if Ian is right, then Conner must be trustworthy. Ian agrees to only show Conner the tunnels until they’re sure he can be trusted, and then they’ll bring him to the observatory. Ian then goes to get him via the tunnels and brings him through the panel in their room.
The five students go to the yellow elevator doors and use the eye in the paperweight to open the door. The elevator takes them to a lab with an array of tools for medical dissection. Gabe goofs around and puts on a pair of headphones, but when he turns them on, he gets a shock. His friends come to his aid, and discover that he can’t remember the last few minutes. They figure the Tower Prep doctors use the equipment to blot out their memories of how they were brought to Tower Prep. Someone comes down on the elevator, and Conner finds a nearly invisible panel with another retina scanner. The eye is sufficient, and Suki impersonates the old man’s voice. The computer greets her as Cornelius Tower and says that it’s been a long time, and lets them in just in time. In the Far East, Cornelius learned the secrets of mysticism. His father came to him in a dream and told of his death, and left him his wealth and an unexplored peninsula of land that he owned. Cornelius suffered from further breakdowns, and dreamed of creating a preparatory for the protection of all creatures. He then traveled the globe collecting near-extinct specimens, creating the occasional hoax to misdirect people from Tower Prep. Most important of all, Cornelius sought to create a haven for special beings who could advance their...
The recording breaks off, and Gabe notes that Cornelius is apparently insane. Suki suggests that the entire thing is one big piece of fiction. On the recording, Cornelius talks of betrayal from within, and corporate lackeys taking over Tower Preparatory, and turning the students into something else. The recording cuts out again, leaving them none the wiser.
Conner suggests they take everything they can with them, since they may not be able to return. The others agree and they go out through the lab. The doctor attacks them, wielding an electric saw, and Gabe ducks into the elevator. It closes behind him, trapping him... and he discovers that he’s not wearing any pants.
Gabe wakes up and discovers that he dozed off in the massage chair in Cornelius’ office. They go out through the lab, and no one attacks them. Once they’re back in the tunnels, Ian starts to tell Conner about the observatory, but Conner says they can discuss it later. He tells Ian to take the stuff there while he gets Suki and CJ back to their rooms.
Ian wakes up in his room and discovers that Conner isn’t in his bed. He hears the jazz music and follows it to an office. Conner is wearing an old-fashioned suit and glasses. Ian wonders how he knew about the door to Cornelius’ office, and Conner thanks him for his help. He says that he has to leave because he’s been found out. There are exiles who want to restore Tower Prep to its original purpose, and sent Conner as a spy. Now he has to leave, but he assures Ian that they’ll meet again Ian wonders if the exiles sent them the dreams, and Conner says that they didn’t, and escape is on all their minds. Ian notes that CJ didn’t dream about escape, but Conner doesn’t respond. He kneels and calls Ian his “liege,” and then tosses a rope up to the ceiling, limbs up it, and disappears.
Ian wakes up from his dream, and discovers that Conner is gone. Headmaster arrives with the Monitors and searches for Conner without success. As they begin a school-wide search, Headmaster asks Ian where Conner is. Ian figures that Conner isn’t who Headmaster thought he was.
Later, the four students go back to the observatory and discover that all of Cornelius’ material is gone. The only thing left is a photo of Cornelius with an old boy. Ian is surprised to realize that he’s the young boy in the photo.