On June 13, In Odessa, Texas, Primatech, the leaders in "Evo" research, are hosting a peace summit for Evos and humans to come together, when the venue is bombed. Mohinder is blamed for the bombing, and over the next year, people with powers around the world are hunted down, believed to be dangerous and untrustworthy. Tommy Clark, a high school student with powers living in Illinois, barely escapes an anonymous meeting for Evos that turns into a slaughter. Noah is working as a car salesman under the name Ted Barnes when he finds out that his memory of the bombing was tampered with. War veteran Carlos Gutierrez finds out that his brother Oscar has been fighting crime as a masked vigilante with super strength in Los Angeles, but when Oscar dies, Carlos is faced with tough responsibilities. In Tokyo, a girl named Miko Otomo finds a sword in her father's study that sends her into a video game world to save him.

Tommy uses his powers to save himself and his friend Emily from Luke and Joanne Collins, who are killing evos, but nearly gets himself caught. Ren Shimosawa finds the game Evernow running on Miko's computer and teams up with her to rescue her father. Wondering why he would need to forget what is coming, Noah returns to Primatech's original location in Odessa with Quentin Frady, a former temp worker at Renautas, the company that bought out Primatech. Going through Oscar's notes, Carlos stumbles upon Oscar's underground railroad for evos escaping to Canada. When Luke and Joanne find themselves teleported to Tommy's old room in Primatech's Level 5, they break out, killing everyone still at the company and taking the files with every Evo's known location.

In the far north, the young Malina uses her power to suppress the malignancy that is approaching. Meanwhile, Molly Walker, who has the power to locate other Evos, has been captured by Renautas. In Yamagato Tower, Miko is captured by a man named Harris. He gives her sword to Erica Kravid, CEO of Renautas, and identifies it as Hiro Nakamura's. At a hospital, Noah finds surveillance video of himself standing over Claire's body, with evidence of Hiro's time jumping abilities. Joanne is eager to chase down the new leads in the Primatech files, but Luke is terrified by signs that he is developing a power of his own. Miko chops off Harris's hand and escapes with Ren, while Harris's hand generates a clone of himself. Tommy's mom finds out that a man has been secretly protecting him. Carlos puts on his brother's mask to become El Vengador, but meets his match in a powered enemy. Erica uses Molly to launch E.P.I.C., a technology that identifies evos around the globe.

When Tommy and his mom end up in a car crash, Tommy teleports her to a hospital before passing out. Noah and Quentin look for a way into the Renautas building, and use Taylor Kravid's frustration with her mother Erica's lies to gain her help. Malina and her invisible companion, Farah, leave the Arctic Circle, and Malina shows an ability to bring plants and animals to life. When Luke reveals his powers to Joanne and burns the list of Evos, she refuses to shoot him, but she walks away from what is left of their marriage. Tommy takes a blood test to see if he can give a transfusion to his mother, bringing federal agents after him. Carlos's nephew José and friend Father Mauricio, both Evos, are kidnapped. In Renautas, Noah finds Molly and a room full of Evos hooked up to machines; Molly takes his gun and shoots herself in the head.

Ren gathers a group of Evernow fans cosplaying as Katana girl at Renautas so that Miko can enter the building undetected. Meanwhile, Tommy is registered as an Evo and injected with a tracking device, and told to stay within a ten-mile radius; he learns that he was adopted. Still inside Renautas, Noah, Quentin, and Taylor find evidence that the company is preparing for the extinction of humankind. One of Harris's clones finds Farah in Canada. Malina tries to fight off his agents, and finds her powers subdued by an Evo who can manipulate shadows, while Harris shoots Farah. Returning home, Luke finally faces the reality of his son's death in the attack one year ago. When Noah and Quentin are captured by Harris, Miko bursts in, taking back her sword and giving them a chance to escape. The man who has been protecting Tommy appears, and tells him that he will help save the world. Renautas scientists reveal that there is less than a week until solar radiation devastates the earth.

Carlos learns about a place that is keeping Evos. Miko and Ren return to Evernow to save the "Master of Time and Space." Tommy runs away to Paris with Emily, but learns that nowhere is safe. Miko meets Noah and Quentin in Renautas, and joins forces with them. They discover that Renautas has harnessed Hiro's power to send what is needed to rebuild the Earth to the future. They learn that Miko is only a program that will disappear when Hiro is rescued and the game ends. Malina meets Luke, and when she sees him try to drown himself, she manipulates the wind to rescue him. Quentin confronts the girl who manipulates shadows, who is his sister Phoebe; she kills him to protect Erica's mission. Harris has Noah cornered when Miko completes the game, releasing Hiro. Noah asks Hiro to take him back to the Odessa peace summit on June 13 to change the future. Though reluctant, Hiro agrees as Erica was harnessing his power for her own benefit. Taylor sends a message to HeroTruther revealing that Renautas kidnapped Evos. Malina opens the envelope Farah gave her to find a picture of Tommy, who Luke recognizes. Emily helps Tommy take out his tracking chip, and they kiss.

On the day of the peace summit, Mohinder Suresh meets with Angela Petrelli, who tells him that she had a vision of the coming disaster and the Evos who can stop it. She told Erica with the hopes of saving everyone, but Erica intends to save only the people she chooses. Hajiro Otomo traps the Hiro of this time inside Evernow and takes his sword. Meanwhile, Noah and Hiro witness the Noah of this time get taken away by Erica's men. Angela takes future Noah to Claire, who is in surgery, but they are told that she died in childbirth. Mohinder gives his Evo research to Molly before Harris takes him to the site of the bombing, and although Hiro rescues him, he discovers that any attempt to stop the bombing will result in a worse future. Past Noah is rescued by Caspar, while future Noah confirms that Claire is dead and says goodbye. Shortly before the bombing, Phoebe Frady releases a massive cloud of darkness that causes a solar eclipse and drains all of the Evos' abilities, after Erica threatened to kill Quentin. Just as the bombs go off Luke and Joanne are separated from their son Dennis. Hiro takes Angela and Claire's children back to 1999 where they will be safe and have time to grow up; they are named Nathan and Malina and Angela has foreseen that they are the only ones who can save the world from the coming disaster. Visited by his mother shortly after the bombing, Tommy is informed that "its starting" and says he's ready. His mother calls him Nathan, revealing that Tommy is Claire's son. Noah sees his future self in the hospital and follows him, as he is about to kill Erica.