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In Los Angeles, FBI Agents Audrey Hanson and Elisa Thayer arrive at the Walkers' home to investigate the murders of James Walker and his wife and the disappearance of their daughter Molly. They discuss the similarities between the murders and those Audrey is investigating as part of the Sylar case. When LAPD officer Matt Parkman locates Molly hiding in a cupboard, the agents become suspicious, and when he mentions Sylar, Audrey arrests him.
At FBI Headquarters in Los Angeles, Audrey Hanson questions Matt Parkman about his discovery of Molly Walker at the crime scene. When Matt manages to convince Audrey that he can hear thoughts, she asks for his help on the Sylar case.
Audrey Hanson meets Matt in the locker room of the Los Angeles Police Department. She tells Matt that she believes Sylar has killed again. She tells him to get out of his uniform and meet her outside.
At the morgue Matt sees the severely burnt corpse of Robert Fresco on the examining table. Audrey believes this is another victim of Sylar, but Matt points out that there's nothing out of the ordinary with the corpse. Audrey tells Matt that the corpse is putting out a large amount of radiation despite no radioactive material having been found at the scene. All they found was a fingerprint that was seared to the bone that matches Theodore Sprague. Audrey believes this is Sylar.
Matt and Audrey arrive at Theodore's residence alone. They search the house and find radiation damage in many places. After entering the bedroom, Audrey finds extremely high radiation levels and they both leave quickly.
Matt gets a call from his wife, which he ignores. He tells Audrey that he doesn't believe the man they're following is Sylar. Matt found an anti-cancer drug prescribed to Karen Sprague by Robert Fresco in the bedroom. Matt and Audrey take a trip to the hospital to visit Karen and find Theodore Sprague at her bedside. Ted tells Audrey that he didn't mean to kill Dr. Fresco. He lost control when the doctor claimed he couldn't help Karen. Matt relays Karen's final thoughts and memories to to Ted before she passes away. The FBI place Ted through decontamination and into a special cell downtown.
Matt learns from his former partner Tom McHenry that Audrey put in a request to have Matt retake the detective exam in a series of interviews to accommodate for his dyslexia. Matt risks losing the opportunity, however, after punching Tom for sleeping with his wife.
Audrey yells at Matt for jeopardizing her investigation by hitting his former partner. She asks Matt if he's suspended, and he tells her he'll work it out.
Audrey and Matt interview Theodore Sprague. Matt learns that Ted also had a black-out after which things started dying, and that he shares the same mark on his neck from the experience. Ted explains that he was in Kansas a few months back having sold a dialysis machine to a university hospital. He went to the hotel bar where he saw a couple from Wyoming, a few professors, and a student from Haiti. The next thing he knew he woke up in his car two days later in Arizona with cuts and bruises on him. Matt realizes that the same Haitian was involved in his black-out, and then several other FBI agents arrive and escort Ted away for transport. One of the agents tells Matt and Audrey that Matt shouldn't be there since his badge was suspended.
At Union Wells High School, Audrey and Matt discuss the crime scene. Matt tells her that it fits Sylar's M.O. and they find a separate trail of footprints and theorize that Sylar may have had accomplices. Audrey tells Matt that they have a suspect, Peter Petrelli, in custody, and they decide to go speak with him.
Peter tells them that he didn't kill Jackie. Audrey tells him that the blood they found on him was his own but asks him to explain why he doesn't appear to have any injuries. Peter refuses to answer their questions and asks if he can go since he's not being charged with a crime. Matt tries to get inside Peter's head but both Peter and Matt experience a disturbing feedback loop from trying to read each other's minds. Peter tells them that if they want to catch Sylar then they need to protect Claire. Matt and Audrey leave and Audrey tells Peter that he'll get out when she gets some answers.
Claire and Mr. Bennet sit in an interrogation room speaking to Audrey. Claire tells Audrey how Sylar killed Jackie and Peter saved her life. After Claire leaves, Matt tells Audrey that he wasn't able to read their minds and that there was a static that interfered with his telepathy. Matt tells her that he heard this static once before at a bar the night before he can't remember the following day. As Matt and Audrey enter a different room, The Haitian, who had been standing nearby, glances around before walking away.
Matt and Audrey stake out Primatech Paper Co. They see Mr. Bennet leave the building and start talking to the Haitian. Matt recognizes the Haitian as the man he saw in the bar before he lost track of the next day. Using a lot of effort, he tries to enter their minds. The effort causes Matt's nose to begin bleeding. He's able to get a single word: Sylar.
On a hunch from Matt, Audrey directs a FBI SWAT team raid on Primatech Paper Co. but fail to find anything incriminating.
Mr. Bennet gives Agent Thayer a parking lot surveillance tape showing that Matt was there every day for two weeks. Agent Thayer scolds Audrey for placing the FBI in a precarious position and tells her that she's going to make sure she is reprimanded for her actions. As Matt and Audrey go to leave, Audrey tells Matt to go home and that they're done.
At Mohinder Suresh's apartment, Mohinder is visited by an FBI agent. Mohinder tells the agent that he's glad the FBI is finally taking the list seriously. The agent tells him that too many people on that list have shown up dead or missing and that if not for records proving he was not in the country at the time, Mohinder would be in a lot of trouble. The agent asks about the list and Mohinder tells him that his father identified a genetic marker that the evolved humans have in common and that he compiled the list using information from the Human Genome Project. He tells the agent that he's been trying to locate them and warn them about Sylar. The agent tells Mohinder that they ran the name and that it was clearly an alias, but that they did find information on one of the other names on the list: Sarah Ellis. Mohinder explains that he tried to find her in Los Angeles and that he's never met her before. The agent asks Mohinder if he's sure, and shows him a picture, revealing Sarah Ellis to be the woman he knows as Eden McCain. He tells the agent that he knows her as Eden and that she lives across the hall, but that he hasn't seen her for a few weeks. The agent tells him that she turned up three days ago in Lake Ramsey dead with a gunshot wound to the head, a suspected suicide.
Ted Sprague is in the custody of the FBI, a suspected terrorist. He reflects back on his marriage to his wife two years earlier, and her eventual decline and death from radiation poisoning. His anger builds, and he explodes, destroying the FBI van, and escapes.
Janice and Matt talk outside their home about Matt's story about Mr. Bennet abducting him. Matt tells her that he needs to find out how Mr. Bennet did this and that he's going to take them all down. Janice expresses disbelief about the story. Matt tells her that he's got to find them and figure out what's going on. He hears Janice think that he should go to the FBI. He tells her that they think he's crazy and he can't go to them.
FBI Agents Quesada and Alonzo arrive at Nathan Petrelli's office and tell him that they want to speak to him about illegal campaign contributions from the Linderman Group. The agents close all the blinds and sweep the room for recording devices as they ask why Mr. Linderman's group, based in Las Vegas, would be helping a NY politician. Nathan explains that his father was an attorney for the group before he died. Nathan tells them that they agreed to not visit in person, and they remind him that he agreed to deliver Mr. Linderman to them. The agents tell Nathan that only they know that he's working with the FBI. They point out that Mr. Linderman has requested a meeting with Nathan and ask him why. Nathan tells them he's still 4 points behind in the polls, that Mr. Linderman is going to tell Nathan how he will help him win, and then tell him what he'll need to do in return for the favor. The agents tell Nathan that they want him to wear a recording device because he's the only one who can get the evidence necessary to put Mr. Linderman in prison. The agents leave and Nathan turns to find Peter in the office. Nathan tells Peter that he's been working with the FBI since Heidi's accident.
At the casino, Nathan speaks into his wire and tells the FBI that Mr. Linderman will be meeting with him in about an hour. The FBI agents monitor the audio from a hotel room in the casino when Jessica barges into the room and shoots them.
Niki explains to Nathan that Mr. Linderman hired Jessica to kill the FBI agents and keep Nathan under control. She tells him that Mr. Linderman's going to offer him a deal which he needs to accept. He is reluctant, but when Niki offers him the choice of running Nathan tells her he can't do that and offers a third option: killing Mr. Linderman. Niki gives him her gun and has him knock her out, so that Jessica will know she isn't in control.
It has been one year since the explosion and Future Hiro, along with Future Peter, plan to break into the Moab Federal Penitentiary, where many special people are being held. The duo stop time to get past the guards and steal the entrance keys.
Once inside, they knock out a couple more guards and hit some switches, which make the cells open. Hiro and Peter enter the general population and begin telling the prisoners to follow a paper crane trail once they get outside which will lead them to safety. A redhead prisoner points to a large, metal door and Peter burns it open. Inside is Niki Sanders. They introduce themselves and leave the building. Outside, some evolved humans and a team of men wearing SWAT protection corner the prisoners, and one agent grabs Hiro by the neck.
At Moab Federal Penitentiary, Peter Petrelli and Niki Sanders come to Future Hiro's aid as he struggles against three evolved human guards, one of whom is somehow able to prevent Peter and Hiro from freezing time. Peter duplicates one of the agent's lightning abilities and attacks the largest agent with it. He summons fire and uses it against an agent with enhanced speed, duplicating her speed to catch her. Niki, using a pole-dancing move, knocks the lightning-wielding guard into the speedster, and the guards are subdued.
As Peter, Ted and Claire walk the streets of New York on their way out of the city, Peter hears Sylar's thought, and realizes that that they are being tailed and that Sylar has learned of Ted's powers. But before they can formulate a plan on what to do, FBI agents, led by Audrey Hanson, arrive on the scene and arrest Ted. Peter grabs Claire and makes them both disappear. Audrey thanks Sylar, who poses as Isaac Mendez, for the tip about Ted.
Sylar later intercepts the police-van transporting Ted and kills him. Audrey arrives on the crime scene of the flipped van, and finds that Ted's dead body is in it. The scene causes Peter and Claire to be stuck in traffic, so they get out of the car and walk up to police boundary of the scene. The three, separately, realize Sylar has struck again.