Jack and Christopher Brandt, a "Comprehensive Scientist" with a vast knowledge of physics, engineering and computer science are in a car looking to find protect Sarah Coppola. However they’re ambushed, and start to fight until a helicopter arrives. Brandt is kidnapped, but Jack manages to escape, and looks at a photo of Sarah.
Following Sarah, Jack puts some glasses on and looks at portals in the sky. He goes to a parking lot and sees an ambulance, which Sarah is taken to. He places a tracker on the ambulance. He follows it to Tokyo Medlab Hospital, which is now abandoned. There, he finds Makoto, who was also looking for Sarah and finds her, but Jack choke holds him and asks him what happened to Christopher Brandt. Makoto has no idea who this is, which makes Jack ask him what he was doing there. Makoto says Sarah asked him to get there, but the Jack doesn’t believe him. Sarah wakes up and hits him on the head, allowing both of them to escape until he finds them and tells them they need to sort things out.
Jack asks Makoto Midorikawa why he tried to kidnap Sarah Coppola, asking if he’s an agent, but Makoto is confused by the comment. Behind a car, are agents sent by Liu Tien Hua who orders the Sarah alive, but the rest dead. Jack sees this and fights back.
Jack puts on some glasses and starts viewing a scenario where he runs to an agent and is killed by the way he shoots. Using this prediction, he is able to dodge the bullets and knock the agent down. He does the same with other soldiers and continues to chase Sarah and Makoto.
Makoto and Sarah hide inside a building, but Jack finds them, so they keep running. Jack finds them and tells them he is done playing hide and seek and holds them at gunpoint. Jack tells Makoto that he still hasn’t answered his question, and asks him what he wants with Sarah again. As soon as he asks this, however, he finds out the portal links are destroyed and left the control field destabilized. Jack looks up in shock to find out the Enlightened were working with her. Suddenly, Makoto and Sarah attack him and leave him unconscious. After they do this, they start running until they see a truck they decide to use for transportation.
Jack is now annoyed and jumps from the top floor to the truck. However, the driver notices and swerves so he falls off. As he starts running, he’s shot by a helicopter, which forces him to leave Dodge. Jack finds out later that the two are going to Kyoto using a train, so he boards the same train.
On the train to Kyoto, Jack is discovered by Makoto, when the latter drops a chopstick and starts chasing him and Sarah. When the two run to a bathroom stall, Jack on the outside believes he found them, but it turns out he's run into Liu's men as soon as they entered a Resistance portal. The men fight while Makoto and Sarah escape. Jack realizes this and is distracted. When they have nowhere left to go, Makoto uses the emergency brake on the train, causing panic, but also enabling them to escape. At the same time, Jack defeats Liu's men, and takes their smart lenses. He also takes a phone and gets a location leading to where Sarah and Makoto were going.
When he got to the facility, he found Sarah and Makoto looking through classified Hulong information and took Makoto and put a knife to his head. Jack tells Sarah to stay calm lest he kills Makoto, and tells her he is confused, since Hulong is looking for her as well. He hands her a phone and asks her what makes her so special. Sarah tells him she is not special, and only wants to uncover Hulong's secrets, which made her a target. Jack is not sure, however, since if that were the case, she would be dead by now. He then asks what her connection to them was and Makoto realizes they want to take advantage of her ability. As soon as he says this, Liu's men enter the facility. Jack jumps to fight them, but is shot and falls.