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After tracking down the woman in the company photo, Peter travels to Primatech in Texas to destroy the virus, but not everything is what it seems. Hiro continues the pursuit of his father's killer. Niki is reunited with Micah, and Claire deals with the aftermath of her father's death. Finally, Maya has to choose to remain with Alejandro, or go with Sylar.

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Mr. Bennet prepares to move his family when he thinks the Company has found them, but Claire doesn't like the idea. Hiro returns to the present and upon discovering his father's death, travels back in time to stop it. Meanwhile, Matt works to master his new mental abilities.

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The events of the missing four months are explored. Mr. Bennet moves his family to California, while Maya and Alejandro discover they must make their way to the U.S. Meanwhile, a mysterious killer stalks the previous generation's Heroes.

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Peter and Caitlin learn about the endstage affects of the Heroes virus. Many of the Heroes work together to fight the nightmare-man. West meets HRG. Hiro and Kensei's journey comes to a head.

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West convinces Claire to teach head cheerleader Debbie a lesson after she deems Claire too ordinary to join the squad. While Suresh faces a serious moral dilemma with the Company, H.R.G. pays his Russian mentor a visit in an effort to locate Isaac's last prophetic paintings. Meanwhile, nearing the U.S. border, Alejandro becomes increasingly uneasy about Sylar's intentions, especially towards Maya. Peter and Caitlin's search for a mysterious doorway he painted ultimately leads them to a surprising place. In feudal Japan, while attempting to repair history, Hiro struggles with his feelings for Kensei's "princess" Yaeko.

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More paintings by Isaac are found and researched. We learn something about Mohinder's past. We meet more new heroes. A woman named Elle is searching for Peter. Ando looks for Hiro in the past. Matt looks for the man in Molly's dreams. HRG takes another step in hopes of protecting his family and himself.

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At a local fast food restaurant, Monica Dawson begins to experience some new abilities. Angela Petrelli makes a shocking confession as new information concerning past heroes is revealed. Matt has Molly locate the "boogyman" on a map, but the results are terrible for everyone. Across the border, Maya and Alejandro make a startling discovery.

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Suresh finds an undiscovered Issac Mendez painting that shows someone's death; Maya frees Alejandro from a Mexican jail; in the past Hiro discovers something new about Kensei; and Niki and Micah leave Las Vegas to get away from their past.

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Matt seeks allies against the new Hero killer. Claire encounters a student with powers. Maya and Alejandro enter Mexico and find their powers more of a hindrance then a help. Suresh tries to locate the Haitian. Hiro works to contain the damage caused by his journey into the past. Peter falls in with Irish gansters who taunt him with a box which contains his past. Kensei's power will be revealed.

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Kisah di episode ini merangkum kejadian yang terjadi 4 bulan setelah akhir musim pertama. Keluarga Bennet (Noah, Sandra, & Claire) pindah ke California, di mana Claire masuk ke sekolah yang baru. Di sana, Claire menghadapai tekanan untuk tidak terlalu menonjolkan dirinya karena ayahnya menganggap hal itu berbahaya. Selain itu, Claire bertemu dengan seorang pemuda teman sekolahnya yang benar-benar tak terduga. Hiro, terdampar di masa lalu dan bertemu dengan pahlawan pujaannya, Takezo Kensei. Pada episode ini juga ditandai dengan kehadiran dua orang Honduras kembar, Maya dan Alejandro Herrera yang menjadi buronan karena dituduh sebagai pembunuh. Mereka dalam pelariannya ke AS untuk menyembuhkan "sesuatu" yang menimpa Maya.