While the team is working on retrieving the fourth card of scylla, Mahone is arrested for attacking police officer and imprisoned in a police station. After confronting Self about his investigation into the General, Wyatt notices a parking pass on Self's car; he stops by the station and finds Mahone. At the warehouse, there is a disagreement among the members about if they should rescue Mahone, and Michael decides to break him out during his arraignment. T-Bag's flees the Gate company after his co-worker accuses him of fraud, but before he can leave the hotel, Gretchen knocks him down and points a gun to his head, demanding to know who he is.

Claire is distraught that she isn't able to feel pain; while she is to get hit by a train, future Peter sweeps her away. Elle finds Bob's body and realizes that Sylar has infiltrated the company; her electrical discharge knocks Sylar unconscious, causing a power failure, allowing the prisoners of Level 5 to escape. After breaking out the prison, Peter finds himself trapped in one of the prisoner's body, and he calls Nathan to warn him. 

Roy has been seeing terrible scenes in his head, including a bus attack with mysterious gas weapon. Walter is recruited to investigate the accident, and he recalls experimenting on a subject allowing messages to be sent into people's head. While performing a surgery on Roy's brain, Walter alters his brain to receive voices instead of images, and the information he received helps Agent Dunham to track down the culprit of the bus attack.

Clark saves the passengers from an exploded bus, including his boss, Tess. Chloe helps a homeless girl named Bette, whose meteor power caused the explosion, and invites Bette to stay with her. After Chloe finds out her ability, Bette tries to kill her, but Clark shows up. Bette is imprisoned in Belle Reve, where Tess visits her, offering her to join a team consisting of individuals with meteor power.

In the beginning, it is revealed that future Peter is the assassin who shot Nathan, he puts present Peter in a company facility and sends Matt to a desert. Nathan resurrects and decides not to expose their secrets. Sylar sneaks into Claire's house, brutally ripping her head open, learning the ability to regenerate after investigating her brain. Hiro's father leaves him a formula, which holds the fate of the world, and a speedster steals it, knocking Hiro unconscious. Mohinder discovers the source of their superpowers, the adrenal gland, and he develops a solution which upon injecting will give superpower to ordinary people; he injects a syringe into his arm and gains super-strength and agility.

Cromartie abducts Charley's wife in order to get John. When Sarah and Derek help Charley to rescue his wife, they are outwitted by Cromartie, who traps them in a remote area and impersonates Sarah's voice to gain John's location. Jumping into the river, John barely escapes from him. At the end, Charley's wife finally dies due to excessive bleeding.

Don Self recognizes one of the cardholder from the picture Michael took at the power plant, and Michael hatches a plan to get close to scylla to copy the data with the device. On her way back to the warehouse, Sara notices that the credit card is missing before realizing that someone has been following her. When she arrives at the warehouse, Mahone shows her a picture of a black guy, whom she confirms to be the stalker. Sucre and Bellick enter the Gate company building in search of T-Bag, offering the receptionist 10,000$ for information of T-Bag's whereabouts, but she denies seeing him. An Asian man approaches T-Bag, threatening to kill him if T-Bag can't hand him scylla in three days.

A woman dies after giving birth to a bizarre baby who ages rapidly and dies four hours later. This reminds Walter of a project he researched with his colleague Dr. Penrose. It reveals that Dr. Penrose has made a major breakthrough; he created a subject,having it to kill prostitutes to cut out their pituitary gland, so he can complete his project. Agent Dunham finds out the crime scene, and Peter saves a girl, but Dr. Penrose escapes.

Clark loses his power after the Fortress collapses, and he is now being held in a russian military base. Chloe has developed super-intelligence, and her captor is not Department of Domestic Security, but rather Luthorcorp; they force her to decipher a piece of message, so that they could nail the members of League of Justice. Oliver bribes the russian captain into releasing Clark, and they proceed to rescue Chloe. Ambushed by the guards, Oliver is injected with drugs which controls his mind; he encounters Clark in the hallway, shooting him in the heart. Trying to save Clark, Chloe finds that she loses the ability to heal. In the nick of time, the Manhunter arrives, taking Clark to the outer space, saving him. Now that Clark has his power back, he decides to live a new life.

An airplane lands at Logan Airport in Boston. All of its passengers die from an unknown virus, which causes their skin to melt down. Phillip Broyles leads several federal agencies to investigate the accident; he orders Agent Olivia Dunham to examine a storage facility, where John Scott, who has a romantic relationship with Olivia, is infected with the virus when chasing a suspect. 

To save John's life, Olivia enlists the help of Dr. Walter Bishop, a scientist versed in fringe science who has been incarcerated in a loony bin for 17 years. Walter invents a system, which enables Olivia to communicate with a comatose John. After identifying the suspect, Olivia raids his apartment, arresting him. John is saved, and Olivia finds out that he is working with the criminal. In a car chasing, John's car turns over, and he dies.