Peter travels to the future and adopts a dangerous ability in order to try to save the world. Meanwhile, Mohinder struggles with his continuing evolution from the formula, and Hiro and Ando re-unite with an old enemy.

Three weeks after the destruction of both Primatech and Pinehearst, and the death of Arthur Petrelli, the now-villainous Nathan returns with a vengeance by persuading the U.S. President and the government to round up all people with abilities, leading to Claire, Ando, Hiro, Matt, Peter, as well as Tracy to become fugitives from the people who were their former allies.

After a look into the future, Nathan's shooter is revealed. Matt chases him and winds up in a desert. Hiro receives an important message from his father. Sylar visits Claire. Maya gives Mohinder an idea for his research. Nathan recovers and gets a visit from Linderman.

Matt goes to extreme measures to extinguish Sylar , who continues to torment him. Elsewhere, HRG calls in a favor from Tracy to save a troubled young boy whose misfortunes resemble her own. While Claire and Gretchen are being hazed by their new sorority sisters, they realize pledging might not be their biggest problem.

As Claire becomes immersed into the world of the Carnival, she becomes increasingly suspicious of Samuel's motives. Hiro is on a mission to rescue one of his own, but has difficulty communicating his intentions to Ando.

Sylar goes to the Company and inadvertently releases 12 super-powered criminals in a fight with Elle. Future Peter tries to fix his mistake. Angela takes over the company. Claire learns more about her powers. Hiro and Ando travel to Paris to track down the speedster who robbed them. Maya discovers that Mohinder's injection has changed him. Matt meats Usutu, an African with a familiar power.

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.

HRG and his new partner go to a local bank heist with four villains; including Peter being trapped in one of them. Hiro and Ando track Daphne to Germany, and meet the Haitian. Tracy Strauss goes to New Orleans to find out more information about Niki. Meredith teaches Claire a lesson about fighting. Usutu shows Matt a series of paintings about him.

As Nathan, Claire, Peter and H.R.G. help Angela uncover her past, she reveals the dark secrets that have haunted her for years. Meanwhile, Mohinder learns of his father’s involvement in a long forgotten government operation.

Sylar returns to the Carnival in search of answers, H.R.G. tries to forge an alliance with Edgar and Peter continues to struggle with the loss of his brother.

H.R.G. recruits Matt to help him take down Samuel, as they use his long-lost love, Vanessa, to lure him to them, but Samuel has his own plans for Vanessa in the works. Meanwhile, Hiro and Ando go to extreme lengths to save Dr. Suresh. Elsewhere, Peter's introduction of Emma to his mother brings forth visions of a very grim future.

Hiros life hangs in the balance as his brain tumor worsens, prompting him to subconsciously deal with some of his past decisions. Meanwhile, Sylar pays Claire an unexpected visit to get answers as to why he isn't quite himself. Elsewhere, Samuels plan to impress his long-lost love, Vanessa, takes a terrifying turn.

Villains Knox and Daphne are on a quest to recruit Hiro and others to the Pinehearst fold. Angela and the Company are paralyzed from recent events. Peter goes to Pinehearst searching for answers but is stunned to learn who the founder is. Claire and Sandra go on a mission to save Meredith from the clutches of Doyle, a villain with abilities to control people mentally and physically. Nathan and Tracy try to trace their origins with Mohinder's help.

Following the showdown against Arthur, Nathan and Peter find themselves pitted against one another, and Nathan makes a decision that will have an effect on the entire world. Meanwhile, Sylar holds Claire, H.R.G., Meredith and Angela hostage at Primatech; Ando, Matt and Daphne try to rescue Hiro and find their only hope may lie in Suresh.

When Hiro travels three years into the past, he has a second chance to save Charlie from the hands of Sylar. However, Samuel’s presence serves to complicate Hiro’s mission even further. Elsewhere, H.R.G.’s past with his Primatech partner is revealed.

Peter goes on a search. West convinces Claire to stand up to someone. Hiro struggles with his feelings for Yaeko. Suresh has more problems with the Company. HRG tries to locate more of Isaac's paintings. Alejandro doesn't trust Sylar.

Nathan faces off against Sylar to keep him from meeting the President. Sylar has his own plans for his new partner. Meanwhile, Hiro learns that there are repercussions to regaining his ability. Elsewhere, Matt is forced to go to extraordinary lengths to protect his future with his family.

As "Nathan" starts displaying new powers, he has visions of an incident from his past involving a young girl and decides to investigate. Hiro tries to save a co-worker and learns a truth about himself. Tracy tries to regain her old life and job.

Samuel prepares for new additions to his family, while Lydia warns him of the consequences. Claire discovers that her roommate Gretchen may have a hidden agenda. Meanwhile, Peter finds an unexpected way to connect with Emma, who would prefer to stay distant. Elsewhere, a different side of Sylar emerges as he desperately tries to remember the person he used to be.

Outside a bizarre, gruesome crime scene, Los Angeles beat cop Matt Parkman is the only one who can hear the cries of a missing little girl. Claire almost reveals her secret ability to the entire school after learning that her injury attempt tape has disappeared. Thinking she's going crazy, Niki loses another block of time after waking to find some brutally murdered thugs in her garage, only to be confronted by Social Services about son Micah. While office drone Hiro investigates New York, Nathan confronts Peter following his plunge off a building.

Claire decides to take on one of the villains herself, but she may not be as invulnerable as she believes. Nathan and Tracy search for the truth about their origins. Maya makes a shocking discovery. Hiro and Ando look for help in the most unlikely places.

Nathan learns of his father's plans, while Flint and Knox launch attacks on Hiro, Ando, Peter, and Claire. Meanwhile, Matt tries to revive Angela, Sylar meets with Elle, and Mohinder begins testing of his newest superpower formula.

Fueled by his vision of Emma in grave danger, Peter attempts to rescue Sylar from his worst nightmare. At the carnival, Samuel reveals H.R.G.s secret past in order to bring Claire to his side. Meanwhile, Lauren makes a bold move to put a stop to Samuel.

Everyone bands together to try to stop Samuel from taking the lives of thousands. Peter joins forces with his most unexpected ally to save Emma. Meanwhile, H.R.G.'s life hangs in the balance as he and Claire find themselves trapped underground with oxygen quickly running out. Elsewhere, Hiro starts to come to grips with the decisions he has made and is called into action to help stop a disaster.

Peter falls in with Irish gangsters who know about his past. Hiro works to contain the damage caused by his journey into the past. Kensei's power will be revealed. Suresh locates and cures the Haitian. Matt investigates the murder of Mr. Nakamura. West comes to know of Claire's powers. Maya and Alejandro enter Mexico and find their powers more of a hindrance than a help.