Sylar, still engaged in an unlikely alliance, faces an identity crisis as his newest power begins to effect him in strange ways. Hiro and Ando try to bring down Building 26 as Matt grapples with fatherhood. Nathan begins to unfold a plan to to set things right.
Angela uncovers the dark secrets of her past, while Mohinder learns of his father's involvement in a forgotten government operation.
Someone close to Danko is put in the line of fire as he spearheads the anti-superhuman operation. Meanwhile, Noah's marriage continues to crumble while Hiro and Ando continue their journey to save Matt. Angela faces some demons from her past.
The heroes try to mend their broken relationships as Nathan and Claire seek refuge in Mexico and Peter and Angela hide out in a church. Danko's bid to wipe out the superpowered population intensifies as he unites with a surprising new ally.
The identity of "Rebel" is revealed. Noah wants Danko to let Tracy go in the hope that she will lead them to Rebel. Hiro and Ando continue with the mission that Rebel entrusted to them, to keep the new hero safe.
Sylar finally meets his father (John Glover) during an unusual reunion; Claire considers helping Doyle evade capture, despite their bitter past; the Hunter tries to expose Petrelli family secrets in hopes of usurping Nathan's operation; and Matt garners attention.
After a tip from "Rebel", Matt and Peter hurry to rescue Daphne and find evidence that may expose the government's plans to capture those with powers. Sylar uncovers the truth about his mother from past memories on his father, while the Hunter hatches an explosive plan of his own.
HRG and Matt are thrust into a series of mind games to uncover the truth about Nathan's plans. Peter gets to meet The Hunter in person.
Nathan becomes the focus of an investigation by Homeland Security. Meanwhile, Nathan's agents hunt for Sylar and Luke, who take a road trip to find Sylar's father; Claire tries to protect a man her dad is targeting; and Hiro and Ando go to India, led by Matt's prophetic images.
Matt's paintings reveal a dire fate for someone close to him; Sylar meets a young outcast (Dan Byrd) with abilities who may be able to help Sylar find his dad; and Nathan's new quest has people with abilities on the run.