Months after explosions brought down Pinehurst and Primatech, our Heroes try to put the past behind them and begin new lives. Now powerless, Hiro tries to train a reluctant Ando to be a true superhero. Suresh returns to life as a taxi driver, Peter is back to saving lives, and Daphne and Matt try to live as a normal couple. Claire's attempt to live a regular life is cut short when she uncovers a deadly plot orchestrated by Nathan to track down and capture those with abilities. Meanwhile, Sylar begins the search for his real parents.

Nathan's plans face exposure as Homeland Security begins an investigation under direct orders from the President of the United States. Sylar and Luke embark on a road trip to find Sylar's father, but are secretly being hunted by Nathan's agents. Life gets complicated for the Bennet family as Claire goes into action to protect a young man with abilities from being captured by HRG. Elsewhere, Matt's prophetic images lead Hiro and Ando to India and a mysterious ally comes to the aid of our Heroes.