Claire, back home in California, begins attending college, but is having difficulty adjusting when a mysterious death of a student during the orientation puts her back in the spotlight. In Japan, Hiro and Ando continue their quest to help people with abilities and go so much as to advertise themselves. Meanwhile, Angela fears Nathan/Syler will discover his true identity. Matt tries to settle down back in Los Angeles and raise his son and not worry about unexpected visitors. Elsewhere, Peter is using his ability for good when a mysterious carnival clan, led by Samuel Sullivan, arrives in town which could spell trouble for him and everyone else.

Samuel continues searching for the whereabouts of the soul of his brother. He begins to focus on Peter by using his ink-transparency powers to investigate Peter. Meanwhile, Claire deals with her secret being outed when Gretchen pressures her to tell the truth. But Noah, comes for a visit and immediately suspects that Gretchen knows about Clair's power. In Los Angeles, Matt Parkman continues dealing with Sylar's ghost taunting him and it hinders his latest case of trying to nail a suspected drug supplier. Also, a new 'hero' with powers is introduced; a young deaf woman named Emma, a dispatcher who works with Peter at the New York hospital, whom discovers that she can 'see and hear' sound breaks.

When Hiro travels three years into the past, he has a second chance to save Charlie from the hands of Sylar. However, Samuel's presence serves to complicate Hiro's mission even further. Elsewhere, H.R.G.'s past with his Primatech partner is revealed.