Željko ends up in a Goon Squad cell with Noah after Sylar frames him for the murder of his agents. Their efforts to escape prove easier than expected when Hiro freezes time and releases everyone there. Sylar finally meets President Worf after attempting to woo Claire, beating up Peter and slitting Nathan’s throat. His plan is overthrown, however, when it turns out Peter absorbed Sylar’s shapeshifting ability and masqueraded as Worf. With Sylar tranquilized, Angela and Noah persuade Matt to work an advanced Parkman Whammy that leaves Sylar morphing into Nathan and thinking he really is Nathan. The approximation fools everyone, including Worf, who agrees to fund a new Petrelli/Bennet-led Company.
By way of an 18-hour flashback, we watch Sylar losing his ability to distinguish himself from the people he shapeshifts into, eventually settling on Nathan and plotting to assume the president’s identity. Inbetween, we see Sylar morphing into Aunt Gray and having a conversation with himself (!), averting death even after Željko plunges a knife into the back of his head (!!) and briefly giving Micah a place to stay (!!!). Meanwhile, Matt returns Baby Matt to Janice, then realizes that his dream of a happy family life won’t be an option until he shuts down Goon Squad Central. Which Hiro and Ando were haplessly attempting to achieve until Hiro’s time-freezing gave him a nosebleed and a killer migraine.
Via flashbacks, we learn that the American government once organized a research facility for people with abilities, and that Angela’s family was brought there and studied by Chandra Suresh. After a prophetic dream about an imminent massacre at the facility, Angela escapes with Bob, Linderman and Charles Deveaux. In the present, we learn that Angela’s weather-controlling sister, Alice, has survived all these years and been living in the facility’s bomb shelter. Having learned the truth about what happened at Coyote Sands, Alice disappears, and Angela turns to creating a new Petrelli-led Company. Which will probably be complicated by the fact that Sylar has morphed into Nathan and taken his place as senator.
Sylar shapeshifts into Sandra, breaks Noah’s heart and manipulates him into pointing a gun at the real Sandra’s head. After Željko and Sylar then trick him into thinking he killed an innocent agent, Noah goes on the run. Meanwhile, hellbent on revenge, Matt discovers that Željko’s in a relationship with a former hooker. After Matt fails to go through with his plan to kill her, Hiro saves his ass, introduces him to Baby Matt and reminds him that life is still worth living. Which probably won’t mean much to the bullet-riddled skeletons being unearthed in Arizona, where Angela, Peter, Nathan and Claire convene in an effort to uncover the truth.
Nathan defuses Matt’s bomb and fires Željko, prompting Željko to prove Nathan has an ability by pushing him out of a window. This presumably means Nathan’s also fired, which frees him up to rescue Claire when her free pass expires and agents storm Canine Central. How this will affect Claire’s new job at Sam’s Comics is unclear, but it’s safe to say Claire won’t be smuggling fugitives like Doyle to safety anymore. Finally, Sylar meets Papa Gray, who, in typical Luthor fashion, promptly betrays and attempts to kill his son. After hearing his father’s speech about the meaning of power, Sylar leaves him to die and visits Željko with a dead rabbit. Make of that last part what you will, but it’s almost as awesome as Angela petting her socks.
Sandra discovers that Claire has been hiding Alex, and with her help, Alex evades Željko’s agents and leaves Costa Verde. Sylar and Nuke pull over at an abandoned diner, and we flashback to the day Papa Gray sold Sylar to his aunt and uncle and sliced Mama Gray’s head open. Meanwhile, following a lead from Rebel, Peter and Matt whammy their way into Building 26. They don’t find Daphne, and Matt gets captured, but Peter downloads footage of Nathan’s operation and delivers it to the evening news. Željko retaliates by strapping explosives to Matt’s chest and dropping him off in the middle of D.C.
Peter, Mohinder and Matt capture Noah and force him to recollect his memories of the past month. Through flashbacks, we learn that Noah didn’t know what to do with himself until Nathan recruited him, that Noah and Željko really haven’t been getting along, and that Daphne was brought back to Building 26 alive. In the present, commandos converge on the SuperTrio, Mohinder gets himself captured so that Peter and Matt can escape, and Noah returns to his crafty scheming with Angela. While hiding out at the Apartment of Clairvoyance, Matt paints himself with explosives strapped to his chest and Capitol Hill going up in flames.
Sylar takes Maya and Molly hostage and forces Mohinder to supply him with a cure that restores his abilities. Noah reaches an agreement with Bob that boils down to him resuming his job at The Company and Claire keeping quiet. Niki rescues Monica from a burning building, but gets caught in the fire herself. R.I.P. Niki. Meanwhile, Peter realizes he’s been played by Adam and destroys the lethal strain of the Shanti Virus. Hiro buries Adam in a coffin deep underground and returns to Japan. And then Nathan decides to tell the world about the superpowered population, which someone obviously doesn’t like because they shoot him. R.I.P. Nathan.
Claire scatters Noah’s (fake) ashes and vows to reveal her ability to the world if it’ll end The Company. Sylar and Maya finally reach New York, but it’s minus Alejandro, whom Sylar stabbed in the chest. This isn’t catastrophic, though, because Maya learns to control her ability without her brother. Meanwhile, Monica tries to help Micah retrieve D.L.’s medal of honor from a gang (don’t ask), and Hiro time-travels to 1977, where he witnesses Adam’s first attempt to unleash a strain of the Shanti Virus on the general population. Hiro returns to the present to stop Adam from doing the same again, but finds Peter unwilling to let him decapitate Adam.
Hiro goes back in time to save Papa Sulu, but Papa Sulu’s adamant about dying because it’s destiny and because Hiro’s not supposed to meddle with God’s will. After meeting himself as a 9 year old, Hiro agrees. Matt begins to harness the Parkman whammy, coercing Angela into revealing the name of the one remaining ElderSuper we haven’t already met. Bob kidnaps Claire, and Noah and West kidnap Elle. They trade hostages, but it ends with Mohinder putting a bullet in Noah’s eye. Which is as devastating as it sounds, even after we learn that someone injected Noah with a sample of Claire’s blood so he’d regenerate.