Nathan learns of his father's plans, while Flint and Knox launch attacks on Hiro, Ando, Peter, and Claire. Meanwhile, Matt tries to revive Angela, Sylar meets with Elle, and Mohinder begins testing of his newest superpower formula.
Hiro attempts to delve into Arthur Petrelli's past to uncover the mystery behind him creating a rival company Pinehearst and his hatred towards Angela. Sylar stricken by guilt tries to stop his murderous ways with HRG and Elle vying for his blood. Meredith's training goes up in smoke with the arrival of her brother.
Tracy and Nathan try to save themselves from a dangerous Mohinder who is no longer in control of himself. Sylar is given the task to save Peter from a rival company. Daphne is ordered to kill or be killed. Hiro is still searching for answers.
Villains Knox and Daphne are on a quest to recruit Hiro and others to the Pinehearst fold. Angela and the Company are paralyzed from recent events. Peter goes to Pinehearst searching for answers but is stunned to learn who the founder is. Claire and Sandra go on a mission to save Meredith from the clutches of Doyle, a villain with abilities to control people mentally and physically. Nathan and Tracy try to trace their origins with Mohinder\'s help.
Matt catches a glimpse of the future, Claire closes down on her first villain, but so are others, Peter finds that his visit to the future has changed him, and Hiro and Ando try to bond with Daphne.
Peter adapts a dangerous ability in order to save the world, HRG gets rid of his partner, and Hiro and Ando want to find out who hired Daphne.
Hrg will have a new partner; Hiro & Ando track Daphne to Germany; Tracy Strauss searches for answers about Niki; 4 new villains introduced
Sylar goes to the company where 12 criminals are released while Claire learns more about her powers. Hiro and Ando tries to track down a speedster in Paris.
The first chapter of “Volume 3: Villains” kicks off moments after shots rang out, as the shocking identity of Nathan’s (Adrian Pasdar) assassin and the reasons why the Texas press conference had to be cut short are revealed — immediately throwing Peter (Milo Ventimiglia) and Matt (Greg Grunberg) into unexpected, uncharted territory. With his powers partially restored, Sylar (Zachary Quinto) decides a visit to Claire (Hayden Panettiere) could give him a boost. Meanwhile, in Tokyo, Hiro (Masi Oka) and Ando (James Kyson Lee) are charged with safeguarding a family secret that could split the planet
In Texas, Peter faces off against former friends due to Adam\'Âs misleading story about the Shanti virus. Micah enlists the help of his mother to rescue Monica. Maya is shocked when she learns the truth about her new friend Sylar. Elle tries to make her father proud.