At Building 26's temporary morgue, a suspicious H.R.G. unzips a body bag to check out what Danko insists is Sylar's naked corpse. With a six-inch spike still lodged in the back of his head and no pulse or body temperature, Danko claims Sylar will never get up again. Danko taunts H.R.G., crowing over his kill after only a few months on the job. Maybe H.R.G. didn't want to catch Sylar. Their conversation is interrupted by an agent who informs them that Sandra is waiting for H.R.G. downstairs.
Somewhere in Ohio, Hiro and Ando drive east on Highway 40 with Baby Matt. Hiro is determined to unite father and son, but his plan comes to a halt when the baby cries and the car suddenly stops working. Meanwhile, Matt and Mohinder are holed up in a in a Washington D.C. motel. Mohinder has finally arranged for safe passage to India, and intends to leave by boat from New York City. Matt refuses his invitation to come with. He's been trailing Danko and is set on revenge. He doesn't want to kill Danko, but he does want him to feel the kind of hurt he's caused for so many others.
H.R.G. meets Sandra in a hallway. Sandra is furious. Even though she can't believe a word H.R.G. says, she needs proof that Claire is safe. H.R.G. is distracted, further offending Sandra. He is just explaining that he thinks Sylar isn't really dead, when Danko pops up to introduce himself to Sandra, who isn't falling for his oily overtures. H.R.G. pleads with Sandra to return to Costa Verde, but Sandra insists that she will be staying at the Regency until she lays eyes on Claire.
Danko joins himself in the bathroom, then morphs into a smirking Sylar, who loves the experience of being Danko -- it's fun. Danko is none too happy with Sylar's hijinks. This isn't supposed to be about Sylar finding a clever way to kill H.R.G. Sylar agrees. He's not going to kill H.R.G.; he's going to destroy him. Meanwhile, Angela phones H.R.G., calling him to meet with the rest of her family at Coyote Sands. H.R.G. insists that he has to get to the bottom of the Sylar situation first, and Angela's order to "get out now" falls on deaf ears.
H.R.G. returns to an empty morgue. All the new corpses including Sylar's have already been sent to the crematorium. Having arrived back in New York, Mohinder uses his super strength to pop out the new lock on his old apartment door, only to find that all his possessions are gone. The landlord informs him that a bunch of guys from Homeland Security took everything and instructed him to call when Mohinder or Matt showed up. Mohinder threatens to implicate the landlord, promising he'll be gone tomorrow anyway. Backing off, the landlord tells Mohinder that his father left several boxes in storage in the basement.
Unable to start their car, Hiro and Ando resort to hitchhiking, and are picked up by friendly trucker Sam, who has a mechanic friend in the next town over. When Baby Matt starts crying, the truck immediately comes to halt. Hiro and Ando conclude that when Baby Touch and Go is happy, things go. When he cries, things stop. Back in D.C., Matt tails Danko as he leaves Building 26. Creating fear, Matt pushes Danko, prompting him to check on the person he cares about most.
H.R.G. rushes to the crematorium to find Sylar's corpse in the nick of time. He points his gun at the back of Sylar's head and withdraws the metal spike. When Sylar fails to revive, H.R.G. countermands the cremation order, and hands the spike to an agent, ordering him to send it to the lab for immediate DNA analysis. Meanwhile, Matt spies Danko arriving at the home of pretty Russian Alena Mihailov. She greets Danko with a kiss and pulls him inside. Matt pulls a gun out of the glove box and gets out of the car.
Sandra knocks on the door of H.R.G.'s apartment. Claiming to have heard from Claire a few hours ago, Sandra plops down divorce papers and asks H.R.G. to sign. Shocked, H.R.G. pleads with Sandra not to throw away 22 years of marriage, but Sandra knows that what they have isn't a marriage; it's a cover, so H.R.G. can go around and shoot people. Besides, it's too late -- not only does Sandra not love H.R.G. anymore, she has no respect for him. Sandra leaves H.R.G. in turmoil, waiting until she hits the streets to morph back into Sylar.
Sam is friendly and apologetic, but he leaves Hiro, Ando and Baby Matt back at their car. The guys do their best to amuse the baby, and finally Ando hits on a particular funny face that quells Baby Matt's crying. Hiro is immediately able to start the car. When Ando complains that he can't keep his funny face frozen all the way to New York, Hiro disagrees. Meanwhile, Matt eavesdrops on Danko's conversation with Alena, who thinks Danko is a schoolbook salesman named Jakob. Danko tells her that he has to return to Chicago and takes off.
Matt breaks into Alena's house. When he realizes she's just a normal, decent woman, he loses his nerve and is about to leave, until she sees him. Alena wonders if the escort service sent Matt. Even though she quit working, they don't listen. Matt asks if Danko is her client, and pushes Alena to believe he's Danko's co-worker. Delighted to meet the first of Jakob's friends, Alena asks Matt to sit down for some tea.
Back at Building 26, H.R.G. is about to sign the divorce papers until he realizes that the signature on them isn't Sandra's. He calls the lab to learn the results of the DNA test. The corpse everyone thought was Sylar has been positively identified as shape shifter James Martin. Alena tells Matt that Jakob has a family in Chicago, but has promised to marry her once his children are grown. Matt explains that Danko's story is a lie, and promises to prove it.
While stopped at a gas station, Hiro calls Mohinder, asking for Matt's whereabouts. Mohinder informs him that Matt is still in D.C., but he's changed, having set a destructive course. Mohinder hangs up and plows through his father's boxes, learning that Chandra was part of a 1960s-era government operation, Project Icarus, which took place at Coyote Sands. Realizing their mission is all the more urgent, Hiro puts the pedal to the metal. They take off without noticing Nathan and Claire, who have stopped at the gas station to find a map that will lead them to Coyote Sands.
H.R.G. violently busts into Sandra's hotel room, holding his gun to the back of her head. Despite Sandra's protests, H.R.G. is convinced that she's really Sylar, and that Danko is in on it. When Lyle calls to ask where Mr. Muggles' pills are located, Sandra is able to tell him exactly, establishing herself as the real Sandra. Devastated by the damage he's done, H.R.G. lowers his gun and tries to explain, but according to Sandra, it really is too late.
Danko is stunned when Alena and Matt knock on his apartment door. Danko automatically takes an aggressive tact with Matt, but his cat is out of the bag, as Alena tearfully realizes that he's been lying to her all along. Holding Danko at gunpoint, Matt explains that Danko kills people for a living, forcing him to tell Alena the truth, including how he allowed Daphne to die.
Claiming it's the only way for Danko to understand what he's done, Matt aims his gun at Alena, but Danko insists there's no way he'll change his mind about the program. Unable to shoot Alena, Matt starts crying, drops his gun and asks Danko to "finish it." Danko shoots Matt. Luckily, Hiro appears in the nick of time to freeze the bullet in mid-air, load Matt into an office chair and wheel him away. When time starts up again, the bullet hits the wall. Fingering Danko as a monster, Alena orders him to stay away from her and runs out.
Pretending to be Sylar in H.R.G.'s body, H.R.G. enters Danko's office, offering old Primatech files -- H.R.G.'s been holding out. Depressed over the loss of Alena, Danko claims he isn't surprised, until H.R.G. pulls out a gun and shoves it in Danko's face. H.R.G. knew Danko could never have captured James Martin alone; now he wants Sylar's head on a platter. Danko explains that Sylar has been going on assignments as Agent Donner, leader of Team Six. He should be back in an hour.
Matt tells Hiro that he wasn't looking to be rescued. Claiming that there's a difference between retribution and righteous battle, Hiro explains his very good reason to save Matt's life -- his son. Matt is instantly amazed to meet his progeny. Back at Building 26, H.R.G. puts his gun to the base of Agent Donner's skull, explaining to the rest of Team Six that Donner is actually Sylar, now a shape shifter. When Danko turns coat, pretending that he doesn't know what H.R.G. is talking about, H.R.G. fires two shots.
One of the agents hits H.R.G.'s arm, sending the two bullets into Donner's back. H.R.G. orders everyone to freeze. If they just wait a minute, Donner/Sylar should begin to heal... but he doesn't. Danko pronounces Donner dead and accuses H.R.G. of killing an innocent man. Grabbing Danko and aiming at his head, H.R.G. finally realizes that Angela was right, and then orders the agents to lay down their weapons. Once all the weapons are on the ground, H.R.G. desperately runs for his life.
Danko sends the agents to chase H.R.G. Once they're alone, Donner morphs back into Sylar, spitting the two bullets out of his mouth. In the clear, H.R.G. calls Sandra, but she doesn't pick up. He leaves a message, pledging his love, and explaining that he has to go underground. He'll call again when it's safe. Danko leaves a similar sort of message for Alena, as she gets in a cab with suitcases, leaving her life with him behind. Mohinder starts creating a map of Coyote Sands.
Peter isn't too happy to see Nathan at Coyote Sands, but Angela claims that the family has to come together. She never wanted them to see what happened here, but now she realizes that you have to understand the past in order to prepare for the future. If they want answers they'll have to dig for them. Nathan, Peter and Claire start digging, and by nightfall, when H.R.G. finally arrives, they are just starting to uncover a mass grave full of skeletons with bullet holes in their skulls. Although she claims to have known them all, Angela refuses to state how many there are, merely telling everyone to keep digging...