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 ...
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...
As Hiro's life continues to hang in the balance, he distracts himself with saving the lives of others. Meanwhile, Angela tries to help the new "Nathan" remember his past, at the risk of his remembering too much. Elsewhere, Tracy is determined to get her old job back, but soon realizes that she needs to make more of an impact.
Samuel prepares for new additions to his family, while Lydia warns him of the consequences. Claire discovers that her roommate Gretchen may have a hidden agenda. Meanwhile, Peter finds an unexpected way to connect with Emma, who would prefer to stay distant. Elsewhere, a different side of Sylar emerges as he desperately tries to remember the person he used to be.
Under Samuel's guidance, Sylar starts on a path to rediscover his true identity. Hiro helps Emma accept and understand the great possibilities that go along with having an ability. Meanwhile, Peter enlists HRG to help him find a healer who can save Hiro's life.
Matt goes to extreme measures to extinguish Sylar, who continues to torment him. Elsewhere, H.R.G. calls in a favor from Tracy to save a troubled young boy whose misfortunes resemble her own. While Claire and Gretchen are being hazed by their new sorority sisters, they realize pledging might not be their biggest problem.
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.
Claire is determined to get to the bottom of the Sorority Rush attacks on her own, until H.R.G. intervenes only to realize he may be the source of her troubles. Meanwhile, Peter's new ability is a perfect fit for his job and gives him the opportunity to help Emma accept her new life. Elsewhere, Sylar's battle at gaining full control over Matt's body escalates -- with potentially dangerous implications at stake.
H.R.G. hosts a non-traditional Thanksgiving dinner by inviting Claire over at his apartment for dinner. But the dinner becomes more awkward and uncomfortable when Noah invites his former co-worker Lauren, while Noah's ex-wife, Sandra, also shows up with her newest beau, a younger man named Doug Douglas, whom like her also has a small dog fetish. Clair is also conflicted about where she wants to be, in which Noah invites over Gretchen to try to lift up her spirits. Meanwhile, the Petrelli family gets a surprise guest at their table when Sylar shows up having reclaimed ...
H.R.G. is greeted by some unexpected visitors and Samuel's grand plan begins to come to fruition. Meanwhile, Peter struggles to accept the truth and takes extreme measures to get what he wants. Elsewhere, Claire's journey leads her to an unexpected destination.
Samuel goes off and tries to bring Emma into the fold by manipulating her about how special her sight-of-sound powers are, while back at the Sullivan Brothers Carnival, Claire becomes more suspicious about Samuel's intentions and deals with not only Samuel's right hand, Replicating Man, Eli, but also the Puppet Master Eric Doyle. A delirium-stricken Hiro returns to Japan and tries to convince Ando in code-talk to help rescue Mohinder from a lunatic asylum in Florida where Hiro forcibly placed him for protection from Samuel.
Claire attends Nathan's funeral while Peter struggles with his grief in his own way by wanting to seek revenge. Meanwhile, Noah and Lauren interrogate a captured Edgar for information to where to find Samuel's carnival. Elsewhere, Sylar returns to Samuel's carnival where he and Lydia try to find a way to emotionally get inside the killer's head to make him see what is troubling him.
H.R.G. recruits Matt to help him take down Samuel, as they use his long-lost love, Vanessa, to lure him to them, but Samuel has his own plans for Vanessa in the works. Meanwhile, Hiro and Ando go to extreme lengths to save Dr. Suresh. Elsewhere, Peter's introduction of Emma to his mother brings forth visions of a very grim future.
Hiro's life hangs in the balance as his brain tumor worsens, prompting him to subconsciously deal with some of his past decisions. Meanwhile, Sylar pays Claire an unexpected visit to get answers as to why he isn't quite himself. Elsewhere, Samuel's plan to impress his long-lost love, Vanessa, takes a terrifying turn.
H.R.G. enacts his plan to take down the Carnival with the help of Lauren and Suresh. Sylar visits Matt looking to understand his desire to make a human connection, but Matt has a plan of his own. Meanwhile, Peter warns Emma of Samuel's intentions after his grim vision of the future.
Peter is forced to travel into Sylar's mind to ask for him to save Emma and the two of them find themselves in a limbo state-like deserted city where they try to find a way out. Meanwhile, Samuel tries to further manipulate Claire by showing the past of Noah's in image flashbacks showing his first wife, and the reasons why he came to work for The Company. Also, a wounded Lauren meets with Emma for medical treatment and to try to get her to listen about Samuel's nefarious plans.