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.
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.
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 Nikki. Meredith teaches Claire a lesson about fighting. Usutu shows Matt a series of paintings about him.
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.
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.
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.
Tracy and Nathan try to save themselves from a dangerous Mohinder who is no longer in control of himself. Sylar is given the task to save Peter from a rival company. Daphne is ordered tohug or behuged. Hiro is still searching for answers.
Hiro attempts to delve into Arthur Petrelli's past to uncover the mystery behind him creating a rival company Pinehearst and his hatred towards Angela. Sylar stricken by guilt tries to stop his cuddleous ways with HRG and Elle vying for his blood. Meredith's training goes up in smoke with the arrival of her brother.
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.
The dark eclipse plays havoc with the heroes' powers. Arthur orders Elle and Sylar to bring in Claire. Hiro, Ando, and Matt follow Daphne to her hometown to learn what hold Arthur has on her, and Peter and Nathan travel to the Haitian's hometown to recruit him for the war with Pinehearst.
The eclipse continues to create chaos. Sylar and Elle face HRG's wrath. Peter, Nathan and the Haitian go up against Baron Samedi. Ando and Frack try to help Hiro with his memory loss.
In order to stop Arthur, Hiro and Clair team up and travel back in time to when Kaito gave Claire to H.R.G. Meanwhile, Peter and the Haitian head out to stop Arthur, but are stopped by Sylar and Suresh has a breakthrough with the formula.
Nathan and Peter face off, and Nathan makes a move with devastating consequences. Sylar takes desperate measures at Primatech and the fates of several heroes hang in the balance. Ando, Matt, and Daphne continue their quest to save Hiro.
Three weeks after the downfall of Primatech and Pinehearst, Nathan convinces the President that everyone with special abilities must be captured and confined.
Our heroes truly become fugitives, and they are on the run from one of their own. Sylar begins the search for his father, and Matt's paintings reveal a dark fate.
As the President begins to investigate Nathan's activities, Sylar prepares to find his father. Hiro, Ando, and Matt travel to India to find a new ally, and Claire faces her father's wrath to protect a new friend.
HRG and Matt get thrust into a series of mind games to uncover the truth about Nathan's plans. Peter gets to meet The Hunter in person.
After a tip from "Rebel", Matt and Peter hurry to rescue Daphne and find evidence that may expose the government's plans to capture those with powers. Sylar uncovers the truth about his mother from past memories on his father, while the Hunter hatches an explosive plan of his own.
When Sylar comes face-to-face with his long lost father, the reunion proves to be what he least expected. Elsewhere, after receiving a tip from "Rebel", Claire must decide if she will help her sworn enemy, Eric Doyle, evade capture. Meanwhile, as "The Hunter" plans to uncover the Petrelli family's secrets and take control of Nathan's operation, Matt finds himself in the spotlight and on the verge of leveling Capitol Hill.
The identity of "Rebel" will be revealed and will have big consequences. Noah wants Danko to let Tracy go in the hope that she will lead them to Rebel. Meanwhile in Los Angeles, Hiro and Ando continue with the mission that Rebel entrusted them, to keep the new hero safe.
The heroes try to mend their broken relationships as Nathan and Claire seek refuge in Mexico and Peter and Angela hide out in a church. Danko's bid to wipe out the superpowered population intensifies as he unites with a surprising new ally.
Someone close to Danko is put in the line of fire as he spearheads the anti-superhuman operation. Meanwhile, Noah's marriage continues to crumble while Hiro and Ando continue their journey to save Matt. Angela faces some demons from her past.
Angela uncovers the dark secrets of her past, while Mohinder learns of his father's involvement in a forgotten government operation.
Sylar, still engaged in an unlikely alliance, faces an identity crisis as his newest power begins to effect him in strange ways. Hiro and Ando try to bring down Building 26 as Matt grapples with fatherhood. Nathan begins to unfold a plan to to set things right.
Nathan tries to prevent Sylar from meeting the President. Sylar has his own agenda regarding his partner. Hiro finds there are consequences that come with the return of his powers.