At school, Ian Archer watches as a bully, Dex, pick on a nerdy student, Andrew. Ian finally gets involved and pulls the bully off. Each punch the bully throws, Ian easily predicts and avoids it. He finally puts Dex in a pressure hold and forces him to apologize, but the principal comes out and orders everyone to move away. Ian is the last one to go.
At home, Ian's parents Michael and Lydia learn that he's been suspended and tell him that he needs to keep a low profile and stay out of trouble. When Ian objects, his mother warns him that he doesn't know what he's capable of. In his room, Ian plays an online MMORPG and talks with another player, Whisper 119. She knows him by name and hints that they'll meet again. When Ian complains about being stuck in suburbia, she tells him that things change and then signs off. He turns on the music and puts on his headphones, but hears interference. When he tries to tune it in, he hears several mysterious sounds. He then collapses back onto his bed.
Ian wakes up in a strange bed with teenagers in red jackets telling him to get up for breakfast. Ian asks who they are, and they explain that they're in their room. Ian looks outside and discovers that he's in a dormitory. The other boys, Don, Ray, and Zack aren't surprised to see him panic, and refuse to answer his question when he asks where they are. They explain that he's at Tower Prep School, and warn him that he doesn't have much time to class. They know his name from the sign on his cabinet, and admit that they lost their fourth roommate, Phillips, to the "forest run." All they'll tell Ian that he was in the room asleep when they got there. Don gives him a playing card with a hand-drawn map, and they get the last tone for class on their laptops from Whisper 119.
Ian examines his cabinet and finds his belongings. However, he's unable to call out, and the voice that tells him he's out of carrier range is the voice of Whisper 119. He goes outside and looks around the campus, unaware that someone is watching him from an upstairs window. Whisper 119 announces over the loudspeaker that all new students should attend orientation in 15 minutes. He approaches a girl and asks her about Whisper, and she gives him directions to administration. Ian goes to the administration building and finally finds a chamber with a glowing computer console. There are three screens, two displaying information and one displaying Ian in the room.
Ian runs out, unaware that the Head Master is watching him on the monitors. He runs into the forest and discovers a tall metal wall blocking his escape. When he approaches it, black-clad figures with glowing green eyes watch him from the woods.
Realizing he has no choice, Ian goes back to the administration building. He finds himself in a battle arena where players on roller skates come at him wielding sticks. Ian defends himself and the players stop and tell him he's in the combat zone circle. The coach comes in and separates them, and explains that Ian's being hazed. He directs Ian to the proper building, and refuses to answer Ian when he asks where he is. As Ian goes, he discovers the map he was given has a Joker on the other side.
As Ian goes to the orientation building, he finds his roommates standing there. They insist it was just a joke, and warn him he can't go inside once orientation begins. One girl, a Monitor, comes over to warn Ian that orientation is over. He ignores her and goes inside, and finds students sitting in an auditorium watching a presentation on Tower Prep. The Monitor comes in and tells Ian that the Head Master has heard that Ian is causing trouble. As she takes him back to his dorm room to put on a uniform, he bumps into a girl, CJ, who says she can't stand people who can't get with the Program. Two other kids, Suki and Gabe, watch.
Once Ian puts on a uniform, the Monitor takes him to see the Head Master. The Head Master has a complete file on him, including his psychological profile. He notes that Ian is a loner, and refuses to answer Ian's questions about where he is. Instead he asks Ian why he defended Andrew from Dex, and explains that he really wanted to test himself. The Head Master tells him that Tower Prep is built for students who are ahead of the rest of the world. Ian is to follow a unique program that will develop his potential, and challenge him like he wants to. He concludes by reassuring Ian that his parents know where he is.
Monitor escorts Ian to class, and he asks for answers. She admits her name is Monica and explains where she's from a place where people didn't understand her. He arrives in class, and Gabe pokes fun at him. The teacher, Science, chastises him. CJ and Suki are also in the class. The tone for end of class signals, and Math comes in and starts lecturing them on the next course. Meanwhile, Ian finds a note on his chair that says, "I'm Scared Too." Ian looks around but can't find anyone willing to identify themselves as the person who sent the note.
Ian returns to his class to find his roommates going through his belongings. When he asks for his MP3 player, Ray drops it on the floor. Ian shoves him up against the wall, but they ask if he's sure he wants to do that. He lets Ray go and leaves, saying he's out. He makes his way across the grounds and into the forest, trying to find a way around the wall. The robed figures with the green eyes, apparently night-vision goggles, approach him and Ian hides beneath a tree. He runs through the forest and they follow, until he comes to a cliff overlooking the ocean.
Gabe, Suki, and CJ are using a GPS tracker to make their way through the forest. Ian finds them and gets them into hiding as the figures move by. Gabe explains that nobody has ever met them and returned, and that the students call them Gnomes. Ian suggests that they go back to campus as it's the safest place to be. They introduce themselves and the others admit that they don't know where they are either. CJ explains that they had to fight back, and Ian admits he's glad that they met them.
As they go back, Ian explains what happened to him. Gabe says that he was leaving a meeting with his parole officer, got into an elevator, and heard the same buzzing noise. Suki found herself there after her parents had a fight, and Ian realizes that her name is on the name of the electronics systems at Tower Prep. CJ claims she has no memory of her life before she found herself at the prep school. She explains that she was trying to escape so she could remember her life before the school. When Ian points out she dumped on him earlier, CJ explains that she did it to maintain their cover. Gabe explains that they're all special in some way. Suki demonstrates she can duplicate any voice, and can pass herself off as the real thing with the proper disguise. CJ can read people's body language and determine what they're thinking and feeling.
As they go back, Ian claims that he has no special ability. However, CJ realizes that he's lying, and Ian admits that he's able to see things just before they happen. He suddenly senses a Gnome just as it attacks them. He shoves CJ out of the way and then knocks down the Gnome. As they run, he takes on another Gnome and goes with the others. They get separates and Suki uses her power to distract the Gnomes by imitating the others' voices. More of them arrive and she's forced to run. She catches up to the others, but the Gnomes surround them. Gabe speaks up and starts talking, and CJ explains to Ian that Gabe can talk his way out of anything. The Gnomes, unimpressed, start emitting a high-pitched shrieking noise. Ian has his new friends cover their ears and gets them out, but he trips. He fights back against the Gnomes, takes a few down, and manages to escape.
The others get back to campus and discover that security is on and there are electric eye beams covering the grounds. When Ian arrives, he detects a pattern to the lights and tells them to follow his directions. He talks them across and more Gnomes attack him. He knocks them out and rips off one of their helmets, which bursts into spark. After making his way across the security grid, Ian admits it's easier when he's not alone and goes inside with the rest.
Inside, Ian's roommates are taking a shower when a hooded figure using Ian's advice grabs their clothes and runs outside. They chase after him, naked, and set off the alarms, and Ian calls down to them from his room a second later. Gabe calls Math out to check it out, and the three boys set off the alarms. The students laugh, and Ian assures Math that everything is fine
Suki returns Ian's jacket, and Gabe asks if they should show him. The girls agree and they take Ian to the old observatory where they first met, and the only private place on campus they can meet. Ian checks the telescope and discovers that the stars are out of place. He wonders if they're in the U.S., and Gabe notes that there's no state or country flag. None of them know why they're there, and Ian says that they can worry about that when they escape. Suki notes that CJ has been there all alone, but their parents sent the rest of them there. She wonders what they'll be going back, and if their parents will reject them. Ian says that no matter what else, they'll have each other.
The next day, the Head Master confronts Ian about the incident. Ian insists he didn't see anything unusual, and claims he plans to go along with the Program. He says that the Head Master was right and he likes a challenge. As he goes, Math comes out and points out that someone has left a Gnome helmet on the flagpole. He wonders if they should discipline the students, but the Head Master says that it's only a message from one student, and if they let it go, he'll become careless. When Math wonders if the students might break, Head Master says that the strong ones survive... and that's what they are there to ensure.
As Ian meets the others, he shows them the note. None of them claim to have sent it, and he wonders who sent it. Someone watches them from the window as they wonder who else might be on their side.