Six weeks or so have passed since we last saw our heroes. Samuel is the leader of a carnie troupe who are mourning his dead brother Joseph. He talks of finding others like them to join them. He soon sets his sights on Hiro. Hiro and Ando have set up “Dial a Hero” in Tokyo but on their first mission Hiro becomes frozen in time. When Ando revives him he admits that a doctor told him he is dying. He accidentally jumps back in time fourteen years to the night he was at a carnival. Claire is beginning her first semester at college and meets her high achieving room mate Annie and more down to earth Gretchen. She tries to fit in and be herself but is shocked when she finds Annie dead. Peter is back as a paramedic and using his powers to save all the lives he can. Tracy comes to kill Noah and Danko but Noah tries to talk her out of it. Samuel sends Edgar to kill Danko, which he does. Angela wants to reform the Company but is increasingly worried by Nathan\Sylar’s erratic behaviour. Matt Parkman wakes in the night to find Sylar holding his son and asking where his body is.
Noah finds a key on Danko and enlists Peter to help him use it. He opens a safe deposit box and finds an old compass. Edgar tries to take it but Peter absorbs his power and fights him off. Edgar cuts Noah and takes the compass. In the hospital Noah calls Tracy for support. Matt is back working as a detective and sees his power as an addiction. He refuses to use it and is in a recovery group for using it. Sylar continues to taunt him until he uses his power when he gets jealous. Gretchen is keen to prove Annie was murdered and Claire reluctantly agrees. Samuel convinces Hiro to interfere in the past causing Ando and Kimiko to become lovers. Hiro now sees righting his past wrongs as his new destiny. Samuel looks set to try and “gather” Claire, Peter and Sylar.
Samuel sues Peter, claiming he was injured when Peter pulled him from a train. He fixes the evidence to fool Peter and test his reaction. Peter discovers that his co-workers are now suspicious of him because of his record of rescues. He apologises to Samuel and shakes his hand, absorbing the “compass” power. Samuel is denied entry to the house where he grew up and so he turns the area into a sink hole, killing three people. Sylar tortures Matt from inside his head, forcing Matt to use his powers. Claire tells Gretchen the truth about her power and tells Noah not to interfere.
Angela brings Nathan some childhood objects to try and trigger his memories. What she triggers is Sylar’s power to see the history of an object. Nathan realises that an old girlfriend of his died in an accident which Angela covered up. He confesses to the girl’s mother and she has him killed. Claire encourages Noah to get a job and Tracy confides in him about her insecurity at returning to work. She gets her old job back with Governor Malden but doesn’t feel right about it. Hiro tries to stop one of his employees from committing suicide but can’t seem to change Tadashi’s behaviour. Eventually Hiro realises that it is his own mortality he can’t seem to accept.
Claire and Gretchen get invited to a sorority rush by a girl called Rebecca. Once there Claire is nearly injured by a failing flag and assumes Gretchen was involved. Sylar is interrogated by the police and a psychologist helps him to work out who he is. When they find out that he is Gabriel Gray they try to get him to confess so he escapes. He winds up at the Sullivan Brothers Carnival where Samuel welcomes him in. Peter accidentally takes Emma’s ability and explains to her that she is not alone. She manages to damage her own building while playing her cello.
Samuel encourages Sylar to become a part of the carnival family. Lydia is attracted to him which makes Edgar jealous. Sylar begins to recover Nathan’s memories so Samuel shows him Sylar’s memories. He then tries to get him to kill Captain Lubbock which Sylar won’t do, but Edgar does. Sylar is welcomed into the family. Hiro tries to help Emma see her ability as a gift. He says he learnt his ability to be cheerful in the face of death from Charlie. He adds her to his list and soon jumps three years into the past to see her. Peter visits Noah to ask if he knows a healer who could help Hiro. Noah takes him to see a boy called Jeremy who can control life and death. He has accidentally killed his parents and Noah stays to help him.
Claire and Gretchen are taken to a slaughter house to begin their initiation into Psi Alpha Chi sorority. As they discuss their feelings for one another Rebecca stalks them and tries to kill Gretchen. Sylar takes over Matt’s body for a bit and it scares Matt into sending Janice away. He tries to drink Sylar out of his mind but ends up allowing him to take permanent control. The Georgia police won’t let Jeremy out so Noah calls Tracy. When they get him freed he accidentally kills a man and he returns voluntarily to jail. Vengeful cops murder him and Tracy is so shaken that she considers turning to Samuel. He arrives to level the police station in retaliation.Gretchen
Three years in the past Samuel finds Hiro and warns him of the consequences of saving Charlie. But Hiro proceeds, using Sylar to destroy her brain tumour. But Samuel spirits her away and tells Hiro that he won’t get her back unless he helps him. Also in the past Noah considers having an affair with fellow Company agent Lauren. He doesn’t though because he loves his family.
Noah and the Haitian arrive to prevent Claire’s new sorority sisters from discovering her abilities. But Gretchen can’t take living under threat from Becky and so leaves. Samuel tells Claire that Noah killed Becky’s father and that is why she was trying to take revenge on her. Sylar wakes up as Nathan and confused he flees the carnival and heads to find Peter. Peter is using his new power to heal people. Emma finally steps back into action, using her medical skills to help out. Now it is Matt trying to sabotage Sylar as he heads to New York. Sylar kills a man by the side of the road to show Matt that it is futile to try and stop him. But Matt then forces the police to shoot him so that he can stop Sylar.
Nine weeks ago Mohinder learnt about Samuel Sullivan from his father’s films from Coyote Sands. He built a compass to locate the carnival and was warned away by Joseph Sullivan. Hiro jumps back in time to stop Mohinder from destroying the film and saves his life by giving him a Kevlar vest to wear. Hiro then drops Mohinder into a mental asylum so he can’t prevent Hiro from rescuing Charlie. The Haitian comes to tell Peter about who Nathan really is. Peter and Nathan go to see Matt and Peter heals him. Sylar manages to touch Nathan, leaving Matt’s body as Nathan flies away. Tracy is considering joining the carnival and seeks advice from Noah as her power begins to behave strangely. She finds Claire and they console one another on the lonely life of those with abilities.
Noah hosts Thanksgiving dinner and invites Claire, Gretchen, Sandra, her boyfriend Doug and ex-Primatech employee Lauren. Naturally tensions abound as Claire discusses not returning to school. At Peter’s apartment he and Nathan grill Angela over what she has done until Sylar reasserts control over his body. At the carnival Edgar and Lydia learn that Samuel killed Joseph thanks to Hiro.
Peter takes the Haitians power and seeks out Sylar. He forces Nathan to the forefront of Sylar’s mind. But Nathan realises he is dead and jumps off a building. Noah realises where Claire has gone and he and Lauren work to find her. Samuel dispatches his new right hand man Eli to steal Noah’s Primatech files. Claire and Gretchen are greeted by Samuel and shown around the carnival. Claire decides to stay for a few days and Samuel talks of settling down.
Claire begins to become suspicious of Samuel, especially with Eli creepily watching her. She breaks into his trailer and finds the Primatech files. Samuel seeks out Emma to help him recruit someone with the ability to grow plant life. Hiro returns to Japan, but seems to be talking gibberish. Claire leaves just in time to reach Nathan’s funeral.
Claire is angry with Noah for what he did and asks him not to come to Nathan’s wake. Peter is in deep mourning and leaves the wake looking to be a hero. Claire helps him take down a man shooting up his office. Sylar heads to the carnival aiming for a feast but finds himself unable to kill. Samuel takes him down and offers to put a tattoo on him which will show him where he needs to be. The tattoo leads him to Claire. Edgar comes looking for Noah and gets tazered for his trouble. Noah and Lauren interrogate him and try to persuade him to bring Samuel down for good.
Noah and Lauren track down Vanessa Wheeler, a woman Samuel grew up with and is still in love with. Noah takes Matt to help persuade her to talk to them. She does and agrees to set Samuel up. However he sees it coming and whisks her away to the carnival. Noah tries to mend his relationship with Claire but she is still upset. Angela warns Peter that she had a dream of Emma killing many people. Peter takes her power and sees for himself the destructive power of her playing and Sylar offering to save her. He destroys the cello and Emma kicks him out. Hiro and Ando rescue Mohinder and head to find Noah.
Samuel continues to seduce Vanessa with stories of the past and dreams for the future. He reminds her of her dream cottage out in nature and see that he has created it for her. She still rejects him and he takes out his anger on a nearby town. Sylar ties up Gretchen and asks Claire to help him out in order to save her. Claire escapes and tells Gretchen what she thinks about Sylar only for her to morph into him; his plan all along was to draw out what she really thought. Hiro collapses and is rushed to hospital, in his mind he stands trial for breaking his own heroes code. With his father as Judge and Adam Monroe as prosecution he is sentenced to death but his mother heals his tumour and he lives.
Claire decides to tell Noah about what Sylar did. But when Lauren tells her what Samuel did she races to the carnival to stop anyone from being hurt. She convinces Samuel to give himself up and Noah agrees a trade. But then Eli shoots Samuel and Claire and kills Lydia, masquerading as Noah. Samuel’s plan works to remove Lydia from the picture and turn the carnival against the outside world. Meanwhile Sylar asks Matt to take away his powers. Janice advises Matt to get rid of Sylar once and for all. So Matt traps him in a nightmare and walls him up in his basement. But Peter arrives insisting Sylar must be freed and heads into his mind.
Peter and Sylar are trapped alone inside their minds for what feels like years trying to escape. Samuel shows Claire some of Noah’s old memories to try and turn her against him. Lauren tells Emma what Samuel did but he steps in to stop her. He begins to move the carnival to New York to confront the world.
Samuel sets up the carnival in Central Park and Doyle forced Emma to play cello and draw a crowd. Tracy rescues Noah and Claire from the ground and Lauren helicopters them to New York. Hiro is about to leave hospital when he meets Charlie. Samuel had her taken to 1944 and she has now lived a full life. Sylar knock Eli out and asks Matt to look inside his head to see if he has changed. Matt instructs Eli to return to the carnival and tell the truth. Claire confronts Samuel and with help from Edgar, Noah and Eli convinces everyone to abandon the carnival and leave Samuel powerless. Hiro and Ando transport the carnies away leaving Samuel with no power as he battles Peter. Sylar stops Doyle and rescues Emma. When it is all over and Lauren is feeding lies to the police, Claire decides to tell the truth. She climbs to the top of the Ferris wheel and jumps off, outing those with abilities to the world.