Eddie Kasalivich (Keanu Reeves) is a student machinist working with a team from the University of Chicago to obtain energy from water. They have been trying for quite some time without success but Eddie, while working at home, discovers the secret to successfully obtain energy from burning hydrogen, leaving only water as a residue. The next day in the lab, the machine is perfected by Eddie and everything appears to be working and stable. To celebrate, a party is thrown in the lab. That night after the party, project physicist Dr. Lily Sinclair (Rachael Weisz) tries to leave the lab but her car battery is dead. Eddie offers to take her home as she is obviously intoxicated, so they walk off in search of a taxi. Back in the lab, Drs. Alistair Barkley and Lu Chen are on their computers while a van is seen driving towards the lab. Chen hears a noise and goes to investigate, but is kidnapped by unknown assailants as Alistair also comes under attack.Meanwhile, Lily and Eddie arrive at her house and after making sure she is okay, Eddie heads back to the lab to get his bike. As he arrives at the lab, he sees a suspicious van driving away and detects alarms coming from the lab. He runs inside to find Alistair with a plastic bag over his head (Eddie is unable to revive him) and Chen nowhere to be found. The hydrogen reactor is on and dangerously unstable so Eddie goes over to the computers to try to stabilize the reaction, but is locked out of the system. Realizing the reactor is going to blow, Eddie runs out, jumps on his bike and speeds away as a concealed detonator triggers a massive explosion that destroys the lab and surrounding streets, eight blocks total. As rescue crews arrive, Eddie is questioned by the police and later the FBI about what happened the night of the blast. Upon returning with Lily to their homes, they soon come to suspect that they are being framed as fake evidence is planted in both of their houses.Both go on the run and head to an observatory belonging to Maggie McDermott, an old friend of Eddie's. After resting up they contact Paul Shannon (Morgan Freeman), the man funding the project (along with DARPA), but are almost caught in the process and barely manage to escape. As Eddie and Lily are evading more police, Paul meets with Lyman Earl Collier (Cox) at C-Systems Research complex to discuss the current events. It becomes apparent that the plot to destroy the lab and frame Eddie and Lily for it was orchestrated by this company, and that Lyman is the one who ordered the attack on the lab. Despite some disagreement, Paul and Lyman decide to continue the hunt for Eddie and Lily, a task made easier when Eddie sends a coded message to Paul requesting another place to meet. At this new rendezvous, Paul reveals he was the one who framed Eddie. The meeting ends in an ambush, and Lily is captured as Eddie barely escapes.By tracing the license plate on the van used in the ambush, Eddie is able to track them to the C-Systems Research facility where Lily and Chen are being held. When C-Systems' test reactor fails again, Paul, the scientists and the prisoners all leave the room, so Eddie takes the opportunity to "fix" the system. The next morning, one of the other scientists discovers the working reactor and everyone celebrates. Paul is suspicious, and immediately obtains a download of the fusion data, and secretly gives it to his assistant, Anita, for safekeeping. He then finds Eddie at a computer in the company board room. There, Eddie demands to be let go in exchange for making the reactor work. Paul agrees but Lyman refuses, believing that the reactor already works, so Eddie sets the reactor to explode while sending proof of his innocence to the FBI and blueprints of the reactor to "hopefully a couple thousand" international scientists.Lyman responds by shooting Chen dead, then leaving both Eddie and Lily to die in the explosion as he, Paul, and their staff flee the site, setting lock-down doors on the way. As the base self-destructs and Eddie and Lily manage to (in a feat of ingenuity) make their escape from the reactor room, Lyman is given a fake copy of the fusion data. Paul then shoots Lyman for overstepping the bounds of the program, leaving his body in an elevator to be incinerated in the ensuing inferno. During his own escape, Paul deactivates the containment, letting Eddie and Lily escape. As he is doing this, Eddie and Lily struggle with security over an ascending construction lift, ending in Eddie and Lily climbing aboard it, moments before a blast wave sweeps into the tunnel. Both Eddie and Lily survive the shock-wave to be met by FBI now convinced of their innocence, who take them to safety. Paul departs the scene via chauffeured sedan. He is last seen dictating a memo to Anita. The memo informs the Director of CIA that C-System is "...no longer a viable entity. Will be in contact."