The films starts with psychotherapist Kate (Kari Matchett), detective Simon (Geraint Wyn Davies), a blind girl named Sasha (Grace Lynn Kung), engineer Jerry (Neil Crone), game developer Max (Matthew Ferguson), lawyer Julia (Lindsey Connell), and an elderly woman named Mrs. Paley (Barbara Gordon) trapped in brightly lit cubes, each with six panels on each side which are doors to other rooms. They come across Colonel Thomas (Bruce Gray), who says that they have to solve the code in order to leave the mysterious place. A wall begins to close in on the group. The group escape while Thomas stays behind and handcuffs himself. They realize that the wall is non-physical and evidently dangerous due to Thomas's reaction to it. Kate and Simon watch in horror as Thomas is disintegrated by the wall, the suitcase he was holding reduced to tatters. Later experiences around the cube reveal that gravity can operate in different directions in each room, while Mrs. Paley and Jerry realize that they may be in a tesseract. Kate begins to notice the numbers "60659" everywhere they go.
The group realize that they are connected to Izon, a weapons industry. Mrs. Paley then opens a panel to reveal her and Simon being killed. Jerry thinks that it is a parallel universe, while Max and Julia think it is an optical illusion. Later, while the group are sleeping, Simon realizes that he is in the tesseract to look for Becky (Greer Kent), a missing Izon worker. Meanwhile, Sasha, who has acute hearing, hears a noise and awakens everyone. The group find a floating square in the middle of the room which initially grows into several shifting variations of a tesseract, before expanding into a lethal and rapidly spinning frame.
The group flee into another room, but Jerry is caught and dies after being pulled into the tessaract. Sasha and Kate are separated from the group. Simon starts to suspect that Mrs. Paley is an undercover spy, so he gags and ties her up, but crystal beams start protruding from the walls. Simon tries to save Mrs. Paley, but instead stabs her with his knife and leaves her to die. Max and Julia, disturbed that Simon killed Mrs. Paley, leave him. They start to have sex, but unbeknownst to them, they are in a room where time speeds up, and they age prematurely. Simon, alone and hungry, goes insane. He encounters a parallel Jerry and the missing Becky.
Meanwhile, Kate finds grisly alternate realities in other rooms. Sasha tells Kate that time and space are distorted at where they are; the tesseract will implode and reality is collapsing. She then reveals that she is Alex Trusk, a computer hacker who is responsible for the creation of the tesseract. She also reveals that when she discovered that Izon was actually putting people inside the tesseract, she tried to stop their operation, but was pursued so she "fled into the only place they wouldn't follow." Kate, however, still believes that there is a way out. Kate finds Simon and stabs him in the eye after he grabs her. Simon then appears behind Alex, old and blind in one eye, proving Alex's time theory. Alex claims that they "are all dead", which causes Simon to snap her neck. Kate finds that the tesseract is shrinking, and kills Simon with the knife. She looks at the numerous watch duplicates of Jerry's and realises that "60659" is the time that the tesseract will implode (6:06:59) and that she is there to take back Alex's necklace, filled with confidential information on Izon. The hypercube starts wearing away, and Kate opens a panel in the bottom, revealing a black void. At 6:06:59, she jumps in, just when the Hypercube implodes. Kate wakes up in the hands of Izon authorities. She gives them the necklace and is executed. Izon authorities then report that "Phase 2 is terminated".
The longer alternate ending included in the special features on the DVD reveals the "owners" to be the government; in the shorter version it is unclear who they are, but it is assumed they are Izon. Kate is executed in both versions, but she is praised for being the first operative to make it out alive. In the alternate ending it is revealed to Kate that she was in the Hypercube for just six minutes and fifty-nine seconds. It was an experiment used for quantum teleportation.
The original screenplay written by Sean Hood, which was subsequently rewritten by Producer Ernie Barbarash, had substantially different plot, theme and characterization, as well as a set of over 70 production illustrations, which visualized quite different traps, environments and four-dimensional concepts.