Isaacs horrible predictions begin to unfold, and the ordinary people with extraordinary abilities face moments of pain and peril in Kirby Plaza with unflinching heroism as the first volume of Heroes comes to a close – and the next one begins.

Nathan is poised to become a member of Congress, but must consider those he loves and the advice of his mother and Linderman. Hiro learns of his lineage from his father, and prepares to face Sylar to the death. Peter and Ted attempt to leave New York before the explosion. Matt and Mr. Bennet learn the truth behind the Companys tracking system.

Hiro and Ando are more determined than ever to stop the explosion. Nathan takes surprising steps to win the election. Jessica and D.L. learn how their family fits into Lindermans plans. Sylar visits his mother. Thompson brings someone new into the Company. Side story about Sylar.

Hiro and Ando find themselves five years after the destruction of New York City. People with extraordinary abilities are labeled as terrorists and are being registered, hunted, and killed. Hiro and Ando meet up with darker versions of the other heroes in preparation for a showdown with the President. This includes a darker side of Matt, a Jessica/Niki with a clear winner in their battle, a brown-haired Claire, future version Hiro, and a changed Sylar.

Linderman reveals his vision of the future to Nathan. Mr. Bennet is held captive by Candice and Thompson, while Sylar captures Isaac. Claire meets Peter again and sees her father for the first time. Hiro meets someone unexpected.

With the election looming, Nathan has a disturbing meeting with Linderman and faces a difficult decision. Niki tries to stop Jessica. Hiro finds the sword with help from Nathan and Ando, but then discovers a dark future. Claire finds answers while her surrogate father gets into trouble with Primatech. Sylar faces off against Mohinder and Peter.

Matt and Ted take the Bennet family hostage in search of answers. More is revealed about Mr. Bennet, the agency for which he works, and how he adopted Claire. Ted loses control of his powers and burns the Bennets house. The Haitian escapes with Claire. A new person with powers is revealed. Side story about Mr.Bennet.

Sylar travels with Mohinder and obtains a new power. After reuniting with Ando, Hiro makes a difficult choice. Mr. Bennet and The Haitian unsuccessfully try to capture Claude and Peter, and Claude decides he must abandon Peter. Ted Sprague, Matt, and a new hero seek answers about the marks on their necks. When Mrs. Bennet is taken to the hospital, Claire reveals to Mr. Bennet that she does not trust him. Peter unlocks his powers and faces off against Isaac, which results in tragedy.

While in a coma, Peter has another vision which is too disturbing for him to face alone. Hiro begins his quest for Kenseis sword. Claire begins to rebuild her life.

Claude serves as a mentor for Peter and forces him to reevaluate his relationships with his loved ones. Claire reunites with her birth mother, Meredith. Hiro tries to explain his mission to his father and sister, who have other plans for him. Sylar escapes and pays a visit to Mrs. Bennet. Niki gets out of prison, but she finds herself imprisoned by Jessica.