Four months after Sylar was stabbed through the gut and Peter exploded in the sky we rejoin the action. Mohinder is giving lectures on a virus which is killing people with special abilities. He is recruited to work for the company by a man called Bob who can turn objects into gold. Mohinder is working with Parkman and Bennet to bring down the company. Matt is divorced and bringing up Molly in Mohinder’s apartment. She is having terrible nightmares. Noah has relocated his family to Costa Verde, California. He insists Claire fit in at school and not draw attention to herself. But she makes an impression on a boy called West who can fly. Hiro finds that Takezo Kensei is a greedy English con man. Nathan Petrelli has driven his family away with his drinking and mourning over the supposedly dead Peter. Peter turns up in Cork, Ireland, unaware of who he is. Kaito Nakamura and Angela Petrelli get left photos of themselves with the mysterious symbol on. They both understand it as an assassination warning. Ando tries to help but Kaito is thrown off the roof of the Deveaux building. Finally newcomers Alejandro and Maya are desperately trying to reach New York and Chandra Suresh. They want an answer to why Maya is able to kill groups of people without meaning to.
Hiro takes on the role of Kensei himself and wins the affections of Yaeko. He tells the real Kensei who is then shot in revenge. But it seems he has the power of regeneration. Claire wants to explore her powers but Noah warns of her of what the company would do if they caught her. She cuts off her toe and it re-grows but West sees it happen. Parkman investigates Kaito Nakamura’s death by interviewing Angela Petrelli. She is attacked by the mysterious killer but survives thanks to Matt’s intervention. Maya and Alejandro head further north and receive help from a family friend. Mohinder is sent to Haiti to help a new victim of the virus. It is the Haitian and once cured he heads to California to help Bennet while Mohinder lies to the company. Peter saves Ricky’s sister Caitlyn from some local thugs. But it starts a feud which Ricky insists Peter help them with. He holds the documents which they found with Peter as collateral.
Hiro forces Takezo to realise his destiny by depositing him in front of the 90 Angry Ronin. He returns safe with the fire scroll but Hiro won’t yet leave him on his own. He sends notes back in time for Ando to read. West shows Claire that he can fly and they kiss. Then she sees the marks on the back of his neck and he tells her of the man in horn rimmed glasses who abducted him. Niki takes Micah to his family in New Orleans while she turns herself over to the company to be cured. Sylar wakes up with Candice looking after him. He has no powers and he finds he can’t take hers when he kills her. He is trapped somewhere in a huge forest. Peter helps the Irish gang steal some money and then saves them from a traitor, earning their trust and the affections of Caitlyn. Alejandro is arrested for trying to steal a car. Maya breaks him out by using her power to kill the guards. Mohinder finds the last of Isaac’s last paintings and sends it to Noah. It depicts him being shot through the eye while Claire kisses someone in the background.
Maya, Alejandro and Derek find Sylar lying in the middle of the road. Maya shows him her book and he tells her that he knows Dr Suresh. Derek discovers a newspaper with details of the murders and Sylar kills him in order to stay close to Maya’s power. Angela Petrelli confesses to killing Kaito to avoid the police discovering anything more. Parkman and Nathan share information to try and find out who really did it. Nathan has the full photo of the company founders and Parkman sees his own father in it. He asks Molly to find him but she says he is the man who haunts her nightmares. When she does find him he traps her somehow and her body goes into shock. Claire and West go on a date and she begins to trust him. She tells Noah that she has started cheerleading again in order to cover her lies. Micah is living with another hero in Monica Dawson who has the ability to copy other people’s actions.Derek
Micah encourages Monica to test her powers. Mohinder takes Molly into the company to see if they can help her. He meets Niki there who is struggling to be cured of her multiple personalities. Matt and Nathan head to Philadelphia and confront Parkman senior. He tricks them into living in their own nightmares while he escapes. Ando takes Hiro’s scrolls to an expert who helps him read them. A girl who can fire electricity out of her hands appears in Cork asking after Peter. She kills Ricky when he lies to her about Peter’s whereabouts.
Yaeko discovers that Hiro has powers and is the real Kensei. Takezo sees them kissing and betrays them to White Beard. Peter and Caitlyn go to Montreal and find a note from “Adam.” They accidentally jump a year into the future to find New York evacuated. Noah and the Haitian torture and kill Ivan (who works for the company) and are able to retrieve the rest of Isaac’s paintings. Claire and West use their powers in public to humiliate Debbie and get Claire onto the cheerleading squad. Sylar convinces Maya to use her powers to get them over the US border but Alejandro is deeply concerned. Bob asks Mohinder to test a virus on Monica but he refuses. Bob helps Monica but does assign Niki to keep Mohinder in line.
Hiro and Yaeko escape Kensei’s clutches. Hiro returns and destroys White Beard’s guns. He returns to the present where Ando tells him of his father’s death. West invites himself round for breakfast and Claire has no time to explain before he sees Noah and freaks out. Nathan and Matt come to see Bob and tell him that Maury is on his way to kill him. Bob explains that it is really Adam Monroe who is behind the killings. Maury fools Niki into attacking Bob but she injects herself with the virus to stop from hurting anyone. Matt manages to stop Maury and trap him in his own nightmare. Mohinder finds that his blood can not cure the strain of virus which Niki has. Bob tells him to get Claire Bennet because her blood can cure the virus. Mohinder tells Bob of Noah’s plans to bring down the company. Peter and Caitlyn discover that the Shanti virus has wiped out 93% of the world’s population. Peter ends up accidentally jumping back to Montreal in the present and there he meets Adam Monroe or as we know him Takezo Kensei.
Adam tells Peter that the Haitian took his memory. But that he can repair his mind using his healing ability. By focussing on his love for Nathan he is able to recover his memory while we see what has happened to some of our heroes in the past four months. Nathan was badly burnt by Peter’s radioactivity. Peter took him to hospital before being abducted by Bob and Elle, his daughter. They convince Peter to let them take away his powers so that he can’t hurt anyone anymore. In the neighbouring room is Adam who says he has been there for 30 years. He convinces Peter that they are keeping him prisoner and to stop taking the medication they give him. He does and they escape. Adam uses some of his blood to heal Nathan and they run away from Elle and the Haitian. The Haitian catches Peter but takes his memories to give him a chance at a new life. Meanwhile DL becomes a fire fighter and Niki also takes medication given to her by Bob. The side effects are bad and so she stops taking them. When she does Gina, another former alias takes over and leaves DL for LA. DL follows and beats up her new boyfriend who then shoots DL in a nightclub. Alejandro is marrying a girl who Maya doesn’t trust. Maya finds her having sex with her ex and it triggers her first mass murder. Later Alejandro finds her and tries to hand her over to the police. But it is then that he realises he is connected to her and has the power to resuscitate people.
Claire refuses to leave and so Noah ends up enlisting West’s help to save her. He turns the tables on Mohinder who tries to catch him. During the conflict Noah captures Elle, just as Bob heads to the Bennet house and abducts Claire. They agree an exchange but in the end Mohinder shoots Noah just as Isaac’s painting predicted. Hiro returns to the night his father died in order to save him. But his father assures him that his time has come. Hiro stays to see who his father’s killer is and is shocked to discover it is Takezo Kensei. Parkman discovers he can plant thoughts in people’s minds to force them to do what he wants them to. He uses it to get answers from Angela Petrelli.
Sylar helps Maya control her powers. He convinces her that she doesn’t need Alejandro anymore and then kills him. Bob brings Claire her father’s ashes as she struggles to deal with his death. Claire finds Elle following her and threatens to tell the world about what she can do. Mohinder uses Claire’s blood to cure Niki’s virus but on the way there he gets a call from Sylar who has reached his apartment. Peter and Adam go to visit Victoria Pratt who developed the deadly strain of the Shanti virus. Peter reads her mind to discover that the virus is in Odessa and then Adam frees her in order to kill her. Hiro learns about the creation of the virus and heads to Odessa to destroy it but he is confronted there by Peter.
Peter stops Hiro and Parkman from interfering as he allows Adam to take control of the virus. Nathan finally manages to convince him that Adam shouldn’t be trusted and he destroys the virus. Meanwhile Hiro takes Adam away and buries him alive. Sylar kills Maya and forces Mohinder to demonstrate the cure on her. When Claire’s blood restores her he runs away with it just as Elle bursts in and almost stops him. Niki and Micah go to help Monica who is tied up in a house which is about to be burnt down. Niki saves her but apparently dies in the fire. Noah agrees to go back to work for the company in exchange for Claire being left alone. Nathan holds a press conference to tell the world about his abilities but is assassinated as he does. Angela Petrelli knows who it is though she warns that “Pandora’s Box” has been opened. Sylar uses the cure and regains his powers.