Makoto arrives at the scene of an explosion at Hulong and is greeted by his boss. It is revealed that he is a special investigator. He has the power to see memories of whatever he touches, which is what would be known as a psychic investigator in the United States. He touches Sarah Coppola, the only person found and sees what she saw when the explosion occured and starts screaming because everyone got burned up and vanished. The main detective thinks it’s weird because even if they’d been burned up, there would be bones at the scene. However, they are told to leave.
Having left the scene of the explosion, the investigator offers Makoto a drink, but he refuses because “he’s busy”. While at home, Makoto pours himself some tea, but pours too much, causing an overflow. He gets touched by a watch and sees himself as a kid. People thought he was weird when he was younger because of his ability to see memories. He asks himself how Sarah’s case was even possible, and wonders why the Hulong Lab explosion was being covered as a gas explosion. In a chat he’s told a virus is in danger, and that only he can help. Suddenly everything on his computer screen closes.
Makoto goes to Tokyo Medlab Hospital, which is now abandoned, but he’s sent somewhere inside. Jack is also inside sneaking in to see Sarah. Makoto finds Sarah, but is taken by Jack, who 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 man doesn’t believe him. Sarah wakes up and hits him on the head.
Sarah asks Makoto if she knows him, and decides to trust him when he tells her to go with him. He introduces himself and says he doesn’t know why he’s helping her. Sarah has amnesia and can’t remember anything.
A message on Makoto’s phone tells him to go back to the hospital. Makoto suggests going back to Hulong and reminds her of her name. They go to Hulong and Sarah starts walking towards it. Makoto stops Sarah and is taken to a vision of a space-like scene with a broken building. Sarah tells Makoto Hulong works with XM, which can directly affect the human mind. In their hands, it will be used to betray humanity.
It turns out that Sarah is like Makoto, but she needs Makoto to believe because it’s both of them against the world. Makoto tells her he believes, and tells her maybe both of them are crazy. Makoto asks if Sarah wants to go back into Hulong, and she says she does, but Makoto is attacked by Jack, who says they need to sort things out.
Makoto is asked by Jack why he tried to kidnap Sarah, 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 that Sarah be captured alive, but the rest dead. Jack sees this and fights back. Makoto is shot by an agent, and Sarah carries him away.
Makoto and Sarah run from Jack. Makoto asks why he’s chasing them, and Sarah says some people’s natural talents are heightened through XM exposure. Those are people that are Sensitives. Sarah reveals herself to be one too. Her ability is to see the invisible. Makoto suggests hiding inside a building, but Jack finds them, so they keep running until Sarah suggests running up a flight of stairs.
Makoto and Sarah realize Jack has the ability to “Flash Forward” with XM and see different possibilities, so Makoto says he wants to let the inspector know. However, when he opens his phone, he is told he has insufficient time and tells the Ingress app installed on its own and told him to go looking for her to help her.
The ingress app tells Makoto the world is in danger and many force seek to harness the power of XM, and that Jack, who was tracking him, was part of the Resistance, whose portals gave him his power. Sarah reveals XM enters the world through these portals and sees they’re surrounded by Resistance portals, which unlock and give him power. Makoto is scared and asks what he must do, and is told he must choose a faction. He looks at Sarah and chooses to join the Enlightened. Once that is done, he is told he must use an XMP Burster to attack the Resistance Portals. He does it using his phone, but he doesn’t have the ability to see the invisible, so Sarah tells him he’s doing good.
Despite their efforts, they’re cornered by Jack, who holds them at gunpoint and tells them they’re done playing hide and seek. Agents sent by the Liu discuss who fired the bursters and find they have no idea who did it, but it helps them with their job. They also move onto taking down Links. 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 find 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.
Makoto is feeling weak and remembers he had been shot. His vision starts blurring and he suggests going to the police instead. As they reach the police station, the Ingress app tells him the police have been compromised. And suddenly turns off due to instability. A police officer in front of the front door radios he has eyes on “the suspect” and tells him to freeze. Makoto is shocked and starts running with Sarah, while being chased by the officer. Makoto sits down, confused by everything that’s happening.
Sarah reveals she tried to uncover some of their secrets and tells him he’ll be in danger if he’s around her. As she starts leaving, Makoto tells her they’re in it together, pointing out he’s a wanted man. Sarah points out she can’t exactly remember the information Hulong wants kept private, so Makoto reveals he can see memories. Makoto tells her that he might see things she does not want him to see, but Sarah tells him to look for the information.
Makoto first sees what happened during the explosion, but he wants to see what happened before. Makoto flashes back to the present and tells her he saw a lab in a forest in her memories. Sarah remembers it and starts walking towards a portal. Makoto holds her hand and is able to see what she is seeing. Sarah sees the lab and tells him she found where the project started. Both hear police sirens and start running, following the portals.
Makoto and Sarah reach the train station and board a train en route to Kyoto. Unbeknownst to them, Jack is also boarding the train. As the two sit, Makoto closes his eyes, and Sarah puts her hand on his. Makoto opens his eyes, and sees the energy around them. Sarah tells him he is a Sensitive as well.
Sarah brings Makoto and herself food. During their meal, she tells Makoto that she believes his ability to read memories is caused by XM. Adding to this, she reveals she used to research how XM unlocked what they called “Sensitive Abilities” Hulong. She also mentions that if Makoto keeps on using XM, he could be able to enhance his abilities even further.
They arrive at another station, and Sarah looks at a building from inside the train. She tells Makoto to hold her hand and look at the blue portal, which meant it belonged to the Resistance. She mentions that it is powerful, but not to him, because he is an Enlightened.
Makoto drops a chopstick, but as he bends to pick it up, he looks up horrified at Jack and grabs Sarah, while telling her to run from Jack. s they run, Sarah tells Makoto they entered an Enlightened field, and Sarah tells Makoto to use his psychometry. Despite being nervous at first, Makoto uses it and sees Jack and Makoto's men, but mistakenly assumes they're working together. He runs with Sarah to another end of the train, and suggests hiding in a bathroom, while comforting her. When they have nowhere left to go, Makoto uses the emergency brake on the train, causing panic, but also enabling them to escape.
Makoto is astonished by his power, and walks towards an Enlightened field with Sarah. Sarah explains how XM works to Makoto, explaining that the Resistance thinks XM is a threat, so they want to contain it, so they can use it to humanity's advantage. Sarah suggests they move, and starts asking people for a ride.
Sarah and Makoto manage to get a ride and arrive at a popular tourist attraction. There, Sarah is sure they have found Hulong's Kyoto facility. Sarah discovers a hidden path; which makes Makoto wonder how she did it. Sarah reminds him she sees the world differently, with XM enabling her to see far away places, also pointing out she was considered crazy as a child. Makoto mentions this happened to him as well, which often left him thinking he wished he was normal. However, Sarah mentions that thanks to his power, he was able to save them and it also allowed them to meet each other. They near the facility, and Sarah sees a big, red portal. Makoto decides to touch it and is soon in pain, but Sarah is able to push him away and save him.
As they keep searching, Sarah discovers the servers are still running, but when trying to log into the console finds out she is locked out. Makoto tries using his psychometry to see the password, but has used his abilities too much. When he continues pushing, he finds the password and lets Sarah enter it. They find information leading to human mind control, and even found a page with Sarah's information on it. Suddenly, Makoto was grabbed from behind by Jack, who put a knife to his head. Jack tells Sarah to stay calm lest he kills Makoto. 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. Sarah and Makoto run away.