Deep under Primatech Paper (in Odessa, Texas), when Peter is reunited with Nathan, things take a violent turn when they, Hiro, and Matt all quarrel, (thanks to Adam and his quest for the dangerous Shanti Virus). Then, Micah turns to the only person who can help him, his mom, after seeing Monica abducted by a street gang. When Sylar kidnaps Molly and Suresh, Maya learns just how much of a monster he really is. Elle decides to play the part of a hero so that she can get back into father’s good favor.
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Believing that a virus will kill 93% of the world’s inhabitants in the future, Peter and his new friend make their way to Primatech Paper in Texas to destroy it. Niki has to break some bad news to Micah. Monica must fix what is done by putting her powers to the test. Hiro tracks down his father’s killer. Using his mental abilities, Matt tracks down the final person in the Company picture. Nathan discovers that his brother is still alive. Just outside of New York, Maya is forced to choose; Alejandro or Sylar?
Nathan suffers horrible consequences for his heroic doings when all of the heroes are thrown four months into the past. Peter survives the tragic happenings high above New York City, and the Company tags him as a threat, which eventually leads to an ugly confrontation with the Haitian and Elle. D.L. makes the supreme sacrifice for Micah and Niki. Horrifically, Maya’s dark abilities manifest for the first time, further fueling her and Alejandro to America in search of help. An unexpected yet familiar face is introduced.
Peter and Caitlin get first-hand experience in just how dangerous the virus effecting people with abilities can be, when one of his forgotten powers suddenly shows itself, and they are thrown into a crisis. Bob, Matt, Nathan, Niki, and Suresh must stick together in order to fend off the “boogyman’s” wicked attack. In spite of Claire’s attempts to keep them separate, West discovers that the man who once kidnapped him when he was young is her father. Hiro and Kensei’s legendary journey in feudal Japan takes a final dramatic turn. 
After Debbie deems Clair ‘too ordinary’ to join the cheerleading squad, West convinces Claire to seek revenge. H.R.G. visits his Russian mentor in an attempt to find the last of Issac’s prophetic paintings, while Suresh deals with a serious moral impasse with the Company. In the meantime, while nearing the U.S. border, Alejandro’s unease grows about Sylar’s intentions, particularly towards Maya. During their search for a mysterious doorway Peter painted, he and Caitlin end up in a pretty surprising place. Hiro, who is still trying to repair history in feudal Japan, must face his feelings for Kensei’s “princess” Yaeko. 
While a lost Hero in Ireland tries to move ahead of the past, he discovers that a strange woman, Elle, is willing to kill in order to find him. After a horrible attack on Molly by the “boogyman”, Matt and an unlikely ally go to Philadelphia to hunt him down. Monica, the new local hero, struggles to accept her new abilities. After meeting his new partner, Suresh gets an unsettling assignment. H.R.G. must take extra measures to protect his family. Ando tries to piece together what has happened to his best friend historically, while Hiro continues to fix feudal Japan’s past.
