This season begins with our heroes putting their lives back together. Claire finds that her biggest challenge is forgetting her old life and starting college. Hiro Nakamura goes back to his old life in Japan, but discovers that he has a terminal illness and sets out to fulfill his own personal bucket-list.
Claire's attempt to start over at college hits a major snag when she discovers that her roommate has committed suicide - or did she? Living the lonely bachelor life in D.C. and struggling to find purpose, H.R.G. offers to help Tracy get her life back by having the Haitian wipe all memory of her from Danko's mind. Tracy proceeds to Danko's apartment, only to witness his murder at the hands of Edgar, acting on behest of a very unusual carnival ringmaster, Samuel. Meanwhile, Matt has reunited with Janice and their son in Los Angeles, and got his old job back as an LAPD detective. The only problem is, Sylar has resurfaced in Matt's head, and he wants his body back - now!
Ando has been in love with Hiro's sister Kimiko forever, but she hates him with a passion, and thinks Hiro's new Dial-A-Hero venture is a ridiculous waste of money. To further add to Ando's woe, Hiro confessed that he's dying and there's nothing he can do about it, refusing to change the past to save his own life. Unable to control his ability, Hiro disappears. Having cut himself off from his family, Peter is back at his old NYC EMT job, desperate to save as many lives as he can to make up for the sins of the past.
Claire and her new friend Gretchen investigate the death of Claire's roommate Annie, while Noah comes to Peter for assistance. Samuel and Edgar recover the compass, Hiro realizes his new destiny, and Matt is tormented with mental images from a dangerous foe.
Hiro embarks on a new mission to undo the wrongs of the past, and H.R.G. finds a compass, which ultimately leads to the Carnival. Unable to control his ability, Hiro inadvertently time travels 14 years into the past to bump into Samuel at the Carnival. Samuel prompts Hiro to make a small change to events, which ultimately cause Ando and Kimiko to fall in love. Overjoyed, Hiro realizes his new mission is to un-do the wrongs of his past before it's too late. Under orders from Samuel, Edgar retrieves the compass, leaving H.R.G. badly wounded. Luckily, Peter saves the Company man, and Tracy plays nursemaid.
While Sylar emerges from Matt's mind to wreak havoc in his life, Nathan hasn't quite been feeling like himself. Abilities that he didn't know he had are emerging, and his memories don't seen real. Since Peter is AWOL saving lives in NYC, Nathan turns to Angela for advice. Fearing the re-emergence of Sylar, Angela blames Nathan's erratic behavior on mid-life crisis, and recommends that he get himself a fast car and a loose woman. After all, it worked for his father...
Claire's been avoiding Gretchen like the plague, but there's really nowhere to hide in a co-ed dorm. Deciding to trust, Claire finally comes clean with Gretchen, and invites her to be roommates. In California, Matt's trying to fend off Sylar while on a drug bust. When Sylar tricks him into beating up the perp, Matt knows he's ruined his life, and is forced to use his powers to save what's left of it.
Although grief over the death of brother Joseph has left Samuel unsure of his direction, he dons a suit and leaves the carnival to find Peter in New York. Posing as an accident survivor, Samuel sues Peter for negligence. With the help of a deaf file clerk, who's just discovering her ability to see sound in color, Peter locates Samuel at the hospital. Knowing that Samuel wasn't at the accident scene, Peter dismisses him as a scammer, until Hesam explains that the lawsuit could kill Peter's EMT career. Peter speeds through the city to apologize to Samuel in a park. Calling on his skills as a hospice nurse, Peter helps Samuel talk through his grief, earning his admiration. When Samuel leaves to destroy his childhood home, Peter is drawn through the park by ethereal cello music. The deaf file clerk is discovering that she can play the cello like an angel, but when she realizes she's drawn a crowd, she runs off.
Claire visits her father, concerned that he's without a plan, and offers some advice. Sometimes you have to remember who you were to figure out who you want to be. Unbeknownst to anyone except Lydia, H.R.G. starts a file on Edgar. Tracy decides to get her old job back with Governor Malden. But something doesn't feel right -- she wants to help people and Malden clearly isn't a helping people kind of guy. When H.R.G. passes Claire's advice on to Tracy, she's able to find the strength to quit Malden for good.
Overjoyed to learn that Ando and Kimiko are getting married, Hiro promises to stand in for his father and give away the bride. Since the wedding is a year away, Ando insists that Hiro tell Kimiko that he's dying, but Hiro spends his time trying to save a suicidal employee. Finally, realizing he needs to face the truth, Hiro confesses all to Kimiko, only to experience a devastating pain in his head, and then he disappears. Nathan discovers a past he never knew about, involving the accidental death of his first love, Kelly. When Angela admits that she covered it up and wiped Nathan's memory, Nathan tells Kelly's mother the truth, so she has him killed and dumped in a shallow grave. But a fist pokes through the dirt, as Sylar claws his way to the surface!
Claire becomes suspicious of new roommate Gretchen, when it looks like she's created a near fatal accident during a sorority pledge. Stunning Claire, Gretchen reveals her true motive with a kiss! After an argument with her mother, who wants her to quit grieving and rejoin the human race, Emma runs into traffic. Luckily, Peter's on hand to whisk her to safety, gaining her ability in the process. Later at home, Emma finds a cello, courtesy of the carnival, and discovers that her newfound skill has a dark side -- busting walls.
Angela is worried when Nathan is nowhere to be found. Little does she know, Sylar has dug his way out of the shallow grave in the woods, and stumbled into police custody, while in the grips of total amnesia. A rookie psychologist offers to help Sylar regain his life, but when Captain Lubbock discovers a hint off a fingerprint, he tries to take down the man he believes to be Gabriel Gray. Insisting that he's not a killer, Sylar's ability rises up to protect him, and he's able run from the cops... into the waiting arms of Samuel and the carnival.
Realizing that Hiro's life is ebbing away, Peter imports his ability, then teleports into H.R.G.'s bathroom. Does H.R.G. know a healer? Peter and H.R.G. teleport to a small town in Georgia, where the corpses of teen healer Jeremy's parents have just become fragrant. Mad with grief, Jeremy greets H.R.G. and Peter with a shotgun: his ability to heal has turned into the ability to kill. Peter stops time in front of a blast meant for H.R.G., but he's a split second too late! Luckily, H.R.G. is able to coax Jeremy into bringing Peter back to life.
Back in Mercy Hospital in NYC, Hiro can't stay in bed. He prefers to spend his time convincing Emma that she can use her ability to lift up all of humankind. When Peter finally returns with the ability to heal Hiro -- Hiro disappears! Hiro re-materializes in his hospital gown, outside the Burnt Toast Diner, three years ago. Thrilled, Hiro presses his nose against the window to behold the beauty of his great love, waitress Charlie.
Lydia and Samuel watch over Sylar. Samuel is intent upon integrating Sylar into Carnival life, by any means necessary. To this end, he introduces Sylar to Damian, who touches Sylar's head and walks him into the Hall of Mirrors, which play a montage of Sylar's heinous crimes. Despite the fact the Sylar is completely unglued, Samuel welcomes him into the Carnival family, angering an already edgy Edgar.
When the cops insist they'll only release Jeremy to a family member, H.R.G. calls "Aunt Tracy." Samuel tries to convince Tracy that she should bring Jeremy to the Carnival, giving her a compass so she can find her way back "home." When H.R.G. and Tracy lead Jeremy out of the police station, an angry mob gathers, and Jeremy loses control, killing a man. A deputy decides to take matters into his own hands, chaining Jeremy to a pick-up truck and dragging him to his death.
Meanwhile, pledges Gretchen and Claire are kidnapped by Becky and the Alpha Chi girls to take part in a scavenger hunt in an abandoned slaughterhouse as part of Hell Week. Claire realizes that someone's trying to kill Gretchen, and winds up exposing Becky and herself.
In Los Angeles, Sylar takes over when Matt is making love to wife Janice. Matt decides to tell Janice most of the truth, intending to leave the house to keep her safe, but she insists that he stay put -- she'll leave. When Matt starts drinking, he realizes that the alcohol is having a negative effect on Sylar. After a bottle of tequila, Sylar seems to have disappeared, but Janice returns with Greene to find Matt arguing with what looks like himself. Now Sylar is in total control of Matt.
Still wearing his hospital gown, Hiro slips back in time three years to find himself outside the Burnt Toast Diner in Midland, Texas. Elated to see the love of his life, waitress Charlie Andrews, Hiro is determined to save her from her fate, death by Sylar. Samuel appears to remind Hiro of the Butterfly Effect -- he must tread carefully so as not to disturb the time-space continuum. Hiro makes a deal with Sylar: if Sylar will pinch out Charlie's blood clot to save her life, Hiro will reveal Sylar's future. Once Charlie's life has been saved, the happy couple prepare to live happily ever after... but Samuel has a different agenda. Using the last of time traveler Arnold's life energy to stash Charlie somewhere in time, Samuel begs for Hiro's help. Eight weeks ago he did something very wrong... something that resulted in Mohinder's death.
Three years ago, H.R.G. was also eating pancakes at the Burnt Toast Diner, along with co-worker Lauren. They've been meeting for breakfast twice weekly for a while now, and their relationship seems to be veering towards something more than just friends. When Lauren hands H.R.G. a motel key in an attempt to take their relationship to the next level, H.R.G. balks. Someday he wants to be able to tell his family the truth. Rather than risk their working relationship, Lauren has the Haitian wipe her memory.
There's a giant train wreck in New York City, and Peter is rushing around trying to heal everyone he can. The only trouble is, that each time he heals someone, his energy is depleted. Despite the chaos, Emma finally finds the strength to use her medical skills to save the life of a little girl. Afterwards she confesses to Peter that when she was unable to save her nephew from drowning, she quit medical school. Now it's time to go back.
Gretchen is so scared after Becky's attempt on her life that Claire calls H.R.G. to help out. Finding little comfort, Gretchen books a flight for home and leaves school, crushing Claire. Samuel shows up at Claire's dorm, just as Becky corners H.R.G. at the sorority house. Together, they recount the tale of Becky's past. How when Becky was five years old, she witnessed the murder of her father at H.R.G.'s hands. It's not Claire that Becky wants, but H.R.G. When Becky tries to take out H.R.G., Samuel tasers her into submission, but not before H.R.G. throws Claire to the ground as she tries to prevent him from firing on the carnies.
Meanwhile, Samuel wakes up in Lydia's trailer as Nathan. Freaked out, Nathan puts on Sylar's clothes and flies to New York, where he falls into Peter's arms. Nathan's in big trouble and needs help.
Having lost control of her powers, Tracy retreats to H.R.G.'s apartment where Claire finds her mid-meltdown. When Claire tries to help, Tracy inadvertently freezes her. Luckily, Claire regenerates and the girls bond -- it's hard to make friends in the normal world. Thinking she may just give up any attempt at a normal life, Tracy calls Samuel.
Peter escorts Nathan to his first day back at work, where they are confronted by The Haitian. Rather than wipe their minds per Angela's orders, The Haitian sends Peter to a storage facility which holds the answer the brothers seek -- Nathan's embalmed corpse! The brothers decide to find Matt, who is hovering near death in a Texas hospital. Peter heals Matt, bringing Sylar to the surface. With no other recourse, Matt tells the brothers the whole story -- the real Nathan is dead and lying in the storage unit. Seizing control of Matt, all Sylar needs is a touch of Nathan's hand to be restored to his rightful body. In the ensuing struggle, Nathan brushes Sylar's hand, then grabs Peter and flies to the Grand Canyon to avoid the cops. Matt is overjoyed that Sylar seems to have left him for good and sneaks out of the hospital. Although Nathan is devastated to think that he's really Sylar, Peter grabs onto him, assuming his powers, refusing to let Nathan go it alone.
Nine weeks ago, Mohinder is living the good life in India, reunited with his love Mira. But he can't resist investigating a box of his father Chandra's research from Coyote Sands, which contains a film explaining that Samuel's power increases exponentially when surround with other specials. Hoping to put a stop to Samuel, Mohinder finds Joseph Sullivan, still alive. Joseph has been keeping Samuel's power a secret, wants Mohinder to burn the film and return to India. Just as Mohinder is about to burn the film, Hiro shows up to switch it out -- Samuel has told Hiro that he must save the film in order to save Charlie's life. When time unfreezes, Samuel enters the room, demanding to know what's on the film. Mohinder refuses to tell, so Samuel kills him in a burst of emotion and runs off. Luckily, Mohinder revives, since Hiro has outfitted him with a Kevlar vest, saving his life. Hiro explains that Mohinder has to lay low for eight weeks until he can save Charlie, but Mohinder refuses. Samuel is too dangerous. Reluctantly, Hiro makes Mohinder disappear... to a padded cell in a mental hospital!
Three families celebrate Thanksgiving. Peter and Nathan force Angela to tell them the truth about Nathan's death. She confesses that she had Matt force Nathan's personality into Sylar's body. Sylar takes control of Nathan's body and is about to kill Angela, but Nathan rallies, fighting back to the surface, and flies off.
After watching Chandra's film, Samuel refuses to reveal Charlie's whereabouts to Hiro. When Lydia learns that Hiro has visited the past without saving Joseph's life, she convinces him to bring her to the past on the day that Joseph was murdered. Hiro and Lydia witness Joseph's murder at Samuel's hands. Hiro manages to teleport them back to the present before Samuel discovers them, but he knows they were there. At the Thanksgiving table, Edgar accuses Samuel of murder, and is about to get murdered himself when Hiro stops time, allowing Edgar to run off. Samuel calls in Damian to lay hands on Hiro. Once his brains are sufficiently scrambled, Hiro disappears.
H.R.G. shops for Thanksgiving, hoping to bump into Lauren, and invite her to dinner. Luckily, his plan bears fruit, because H.R.G. has no idea how to cook, and Sandra is bringing her new boyfriend Doug. It's a frosty and awkward meal, until Claire drops a bomb: she's quitting school. When Doug suggests that what Claire's feeling is normal, she grabs a knife and cuts into her arm, healing in front of his eyes. Doug faints, and H.R.G. tries to persuade Claire to reconsider, but she won't until Gretchen shows up. The girls make peace, and decide to go on a road trip with the remainder of their Thanksgiving break... to the Carnival!
H.R.G. (Jack Coleman) is greeted by some unexpected visitors and Samuel’s (Robert Knepper) grand plan begins to come to fruition. Meanwhile, Peter (Milo Ventimiglia) struggles to accept the truth and takes extreme measures to get what he wants. Elsewhere, Claire’s (Hayden Panettiere) journey leads her to an unexpected destination. Adrian Pasdar, Zachary Quinto and Cristine Rose also star. Jimmy Jean-Louis, David H. Lawrence XVII, Madeline Zima, Dawn Olivieri, Todd Stashwick and Elisabeth Rohm guest star.
With his brains scrambled, Hiro finds himself in a crowded Tokyo marketplace. Speaking in his own particular code built from sci-fi and comic book references, Hiro apprehends a purse snatcher before the cops bring him back to Yamagato. Kimiko wants to call a neurosurgeon, but Ando realizes that Hiro is trying to tell him something: they have to go to Riverdale Psychiatric Hospital in Florida.
After looking through H.R.G.'s Primatech files, Samuel sets off for the city in search of Emma, leaving Eli to look after Claire. Aware that Samuel has her father's files, Claire starts poking around, realizing that he's up to something. Samuel tells Emma that he sent her the cello, which was originally meant for his first love Vanessa, the girl that got away. Since Emma's music works like a siren song, Samuel asks her to help him flush out homeless Ian, who has the power to green the earth, and has been hiding out in Central Park. By the time Samuel returns to the Carnival with Ian, Eli has found Claire snooping in Samuel's trailer, where she's found a map of a nearby valley. Claire confronts Samuel over Joseph's murder, and demands to know what the map is for. Samuel takes Claire and Ian to the valley, where Ian plies his ability to create a lush new homeland for the Carnival. Samuel invites Claire to stay, but she's ready to go back to her world, returning just in time to attend Nathan's funeral.
Angry at her father for lying to her about Nathan's death, Claire asks him not to attend the wake, where she finds Peter unable to mourn. When Peter disappears, Claire follows him to a shooting rampage in progress in a nearby office building. Peter confronts the shooter, claiming that he knows the feeling: Peter wants to torture the man who killed his brother. Still, the guy shoots Peter in the shoulder. Later, Claire reluctantly heals Peter while laying into him. By refusing to acknowledge Nathan's death, Peter is dishonoring his memory. Peter softens up, and he and Claire promise to always tell each other the truth. Afterwards, Peter has Claire hook him up with West, so that he can regain his flying ability.
Meanwhile, Sylar returns to the Carnival to kill Samuel, but finds that he can't. Samuel sends Lydia to seduce Sylar to find out why. Lydia realizes that Sylar is afraid to die alone, afraid he can't be loved, and in so doing betrays her own secret -- she wants to kill Samuel. Sylar becomes enraged, insisting that he kills because he wants to, but Lydia knows Sylar can't kill because he's impotent. Sylar confronts Samuel, insisting on a tattoo. Strangely, the tattoo turns out to be a portrait of Claire, which indicates Sylar's next destination.
Edgar shows up at H.R.G.'s apartment, but this time H.R.G. is ready for the speedster. He buys out the sushi restaurant downstairs, installs Edgar in the freezer to slow him down and calls Lauren to bring him a truth drug. Taking Lauren's advice that honey is more effective than vinegar, H.R.G. agrees to join forces with Edgar to take down Samuel. It's all going great until Edgar gets wind of H.R.G.'s plans to break up the Carnival family, and speeds off.
Hiro and Ando break Mohinder out of the mental hospital. Mohinder puts Ando up to using his red lightning as electro-shock therapy to unscramble Hiro's brain so he can teleport them out of Florida.
Hoping that Vanessa will lead him to Samuel, H.R.G. enlists Matt to push her into helping them. Samuel uses his power to escape, kidnapping Vanessa and bringing her back to the Carnival. Vanessa is angry, but her connection to Samuel runs deep. He promises to show her a sight of beautiful perfection, and if she doesn't like it, he'll take her home. Having failed to find Samuel, H.R.G. tries to apologize to Claire in hopes of getting his hands on her compass, but she's not ready to trust him yet. Luckily, Lauren is, which she demonstrates with a kiss.
Peter absorbs Angela's power to learn that Emma will use her cello in the future to help kill thousands of people. In his dream, Peter can't save her, but Sylar can. Fearing the worst, Peter smashes the cello, earning Emma's enmity.
After passing out at H.R.G.'s apartment, Hiro is rushed into surgery, a last ditch effort to save his life. While unconscious, he finds himself at the Burnt Toast Diner, now a kangaroo court room, presided over by his dead father Kaito and Adam Monroe. Hiro pleads guilty to using his powers for selfish gain, punishable by death. As Hiro's heart stops in reality, he swordfights with Adam in hopes of going out like a Hiro. Ultimately, Hiro's mother Ishi walks out of the light to heal his brain tumor and bring him back to life.
Sylar isolates Claire and demands that she help him work out his emotional issues. Claire is furious, but when Sylar threatens Gretchen's life, she plays along. Sylar figures they're both alike in so many ways, but mostly, they both use their powers to cut themselves off from other people. Using the ability Lydia gave him, Sylar looks into Claire's soul with a purloined kiss. Claire stabs him in the eye with a pencil and runs to confess herself to Gretchen. Maybe Sylar's right about her. Gretchen morphs into Sylar, who confesses that Gretchen's life was never in danger. Claire is relieved when she finally finds the real Gretchen, ready to take their friendship to the next level...
Having kidnapped Vanessa, Samuel goes all out for seduction. He buys her a new dress and a strawberry milkshake, waxes poetic about their past, and takes her to the fantasy dream house he built for them in the valley. After a deep kiss, Samuel proposes that they embark on a new life together. Vanessa is flattered, but her life is in L.A., Samuel's fantasy isn't real and it isn't hers. His heart broken, Samuel lets Vanessa go, then destroys a small town in a crazy rampage, while the carnies look on.
Upset by his dream of Emma, Peter convinces Angela to tell him where to find Sylar, who's at Matt's, begging for help. Sylar wants Matt to extinguish his powers, so he has a hope of leading a different life. Matt doesn't think he can do it, but promises to try when Sylar threatens the lives of his family. Instead, he creates Sylar's worst nightmare, trapping him in his own mind alone for all eternity. Once Sylar is no longer conscious, Matt stashes him in the basement and builds a brick wall to cover up Sylar's tomb. Peter appears in the nick of time to absorb Matt's power. When Peter grabs Sylar in an attempt to bring him back to avert Emma's disaster, he is plunged into a silent, completely deserted city.
Claire visits H.R.G. with the intention of making amends, surprised to find that only Lauren is there. It's clear that H.R.G. is up to something. Once Lauren tells her that Samuel killed 200 people in his landslide, Claire runs off to warn Lydia, but of course Samuel catches wind of it. Determined to rise from his disgrace to win back the hearts of his family, Samuel agrees to surrender to H.R.G. to spare the carnies, but he's got Eli up his sleeve. From high on the hill, Eli fires on the Carnival people, wounding Samuel, Lauren and Claire, and killing Lydia. Then he captures H.R.G. and blames the whole mess on him. Edgar returns to the fold, devastated by Lydia's death, and Samuel is once again in control of his minions.
Eli appears at Matt's house intending to prevent Peter and Sylar from finding Samuel. Luckily, Peter and Sylar are able to overwhelm the clones and knock the prime unconscious. Still, Matt doesn't want to trust Sylar, but after going into his mind, realizes he has indeed repented during the five years he was trapped in his nightmare. Meanwhile, oxygen runs out in the trailer buried underground. Dying, H.R.G. makes Claire promise that she'll keep her ability under wraps. Just when all seems lost, Tracy flows in to the rescue. Up top, Lauren has a chopper waiting to take them all to the Carnival, now in Central Park, where Samuel's plan is well underway.
Under Doyle's control, Emma plays cello, drawing huge crowds. Samuel has infused his people with excitement for what promises to be their biggest night ever, but Edgar smells a rat. When he finds H.R.G., he realizes they're after the same thing. Sylar manages to save Emma, as Claire goes backstage to explain to the carnies that Samuel draws his power from them, and intends to kill the waiting crowd. When Edgar, H.R.G. and Eli pipe up to expose Samuel as the murderer of Joseph and Lydia, the carnies need no more convincing and hurry away. Furious, Samuel takes the stage to start an earthquake and a stampede. Peter flies in to tackle Samuel off the stage, picking up his power to do battle of moving earth. H.R.G. calls Hiro to teleport the carnies to safety. Samuel finds himself powerless and the Carnival deserted. It's over.
Volume 6: Brave New World opens as Samuel is driven away by an "old company," and Lauren holds a press conference to explain that all the hoopla was merely a ruptured gas main. When reporters crowd around H.R.G. and Claire, she tells them to keep the cameras on her. Breaking her father's heart, Claire climbs to the top of the Ferris Wheel and jumps, then spontaneously heals for all the world to see.