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?
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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.
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 working over at a local fast food join, Monica Dawson starts displaying some amazing new abilities, leaving her brother, grandmother, and cousin in the dark about her findings. As new information about the prior generation of Heroes is unveiled, Angela Petrelli makes a surprising declaration. Matt asks Molly to put her fears with her “boogyman” aside and locate him on a map, with disastrous results. H.R.G. has concerns with the future when he suspects that Claire has found a new boyfriend. Maya and Alejandro make a dismal discovery as they draw closer to the U.S. 
After returning to New York, Suresh is panic-stricken when he discovers an Issac Mendez painting depicting the death of someone he knows very well. H.R.G. and Claire both follow their own personal, secret agendas. Maya, who is focused on making it to the U.S., employs the use of her abilities to help Alejandro escape from a Mexican jail. Ando makes a very happy discovery after returning to his job in Japan. In Japan’s past, just as Hiro writes off his childhood hero, Kensei, he surprises him. Micah and Niki leave Las Vegas in hopes of starting over. Afterward, Niki and a lost Hero independently make sketchy deals in order to reach their goals. Two well-known people with abilities make an unforeseen revisit.
With one individual dead, Matt seeks out some improbable help as the attacks on people with abilities continue. Claire’s attempts to hide her healing power are at stake when a fellow student at her new California high school with a secret of his own comes into play. In an effort to make a fresh start, Niki and Micah leave Las Vegas. Dr. Suresh must locate The Haitian as part of his new job. While continuing their journey to the U.S. border, Maya and Alejandro’s powers prove to be a serious problem to anyone in their proximity. In the meantime, Hiro, who finds himself disappointed with his hero, Hensei, decides to repair any damage his being in feudal Japan may have done to history. Also, another lost Hero finds his way into an Irish gang which holds clues to his past.
The second season of Heroes starts off with the illumination of Peter, Nathan, and Matt’s fates, subsequent to the face-off with Sylar and Peter’s unrestrained nuclear detonation high above NYC. While everyone is attempting to move on, a new, ominous power begins eliminating Heroes. Hiding in Southern California with the family, Claire and H.R.G. try to live as unobtrusively as they can, which turns out to be much harder than at first thought. During all of this, Hiro lands in feudal Japan and winds up meeting his hero, Takezo Kensei. Siblings Maya and Alejandra Herrera strive to make it across the border into the U.S. from Mexico, in an attempt to find help with their dangerous abilities. 
