The third iStory volume is called The Agent. It began being released after the second episode of Volume Four of Season Three of Heroes.

In this iStory volume, each user is able to explore Rachel Mills's experiences as an agent working for Nathan. Each week of story contains one chapter of stories told from first-person point of view. Most of the chapters are told from Rachel's viewpoint; except for part of the sixth, which is told from the point of view of her partner, Jason Pierce, and part of the ninth and tenth, which are told from the point of view of Anna Korolenko. The stories are entirely text based with a button to choose an action at the bottom of each scene. No registration is required to participate.

Chapter 1
Release Date: 10 and 13 February 2009
Rachel Mills has been hired to work for Nathan. She looks at a battered Tracy and recounts how the day went. She had been broken the field training record and was congratulated by Moore, when Gibson showed up and asked her about what happened in Iran. However, their team is called in to recapture all the detainees of the Flight 195 crash at the crash site. While doing so, Gibson is influenced by someone to betray the team, but is killed by Danko.

Chapter 2
Release Date: 17 and 20 February 2009
Still remorseful over Gibson's death, Rachel Mills suffers bad dreams during her job as an agent. She is assigned a new partner, and Danko has her check out a few websites. She contacts her hacker buddy to help decode some barcodes she finds, which contain the message, "Stop this, Rachel." Suddenly, the lights go out and Rachel's loses communication. She gets text messages from Rebel, who proves to know what Rachel can do by sending Rachel a video file of her at Pinehearst. Rebel warns Rachel not to tell Danko what she just found. Rebel also tells Rachel that he needs her to do something.

Chapter 3
Release Date: 24 and 27 February 2009
Rachel is constantly receiving text messages from Rebel, and she does her best to try not to make Danko and her partner, Jason Pierce, suspicious. They are assigned to Costa Verde to capture Alex. While investigating, they are pointed in the direction of Liliane. Rachel and Jason find a laptop in Alex's apartment, though all the files had been deleted by Rebel. Later, Alex's father points a gun to Rachel's head, asking her what she's doing to his son. Just then, a city-wide blackout occurs, and Rachel teleports to the rooftop of the building, away from danger.

Chapter 4
Release Date: 3 and 6 March 2009
Rachel awakes in a motel, having had nightmares again. She and Jason Pierce eat bagels and then head to the Bennet house to investigate Claire. They enter the house and are confronted by Claire and Sandra, but they find no evidence that Alex is there. When they leave, Sandra and Lyle throw them off the track. Rebel then messages Rachel again, giving her an encoded message. Jason cannot understand the message, but Rebel tells Rachel to break each line at 60 characters, revealing an ASCII image of Eric Doyle.

Chapter 5
Release Date: 10 and 13 March 2009
Rachel has several mysterious dreams, inside which her mother, Leona, is mentioned. Back in real life, Rachel chases Eric Doyle up an alley, but Doyle manages to take control of her. The glare in the background prevents Doyle from recognizing Rachel as the person who rescued him the last time they met. However, Doyle does not kill her and instead flings her into a brick wall.

Chapter 6
Release Date: 17 and 20 March 2009
Jason Pierce, having discovered Rachel's ability during a botched mission, calls for his sister, Janey, to accompany him in bringing Rachel in, but Rachel discovers his plan and shoots him. As he collapses, he hears a motorcycle pull up which he thinks is his sister. The girl takes Rachel to an abandoned hunting cabin and they rest there. When Rachel awakens the next morning morning, she introduces herself as Anna and reveals part of the meaning of LAWR. Anna also passes on Rebel's message that Rachel needs to keep working with the government, and a warning that Janey might decide to hunt her brother's killer.

Chapter 7
Release Date: 24 March 2009
Rachel mourns Jason Pierce's death, but when she is assigned to a new mission, she heads to New York City to check in. Her commander briefs her, and she and Anna meet an old man named Abe and his many followers. Abe has a special ability, but Rachel decides they need to flee. She plans for them to use the back fire escape while she seeks out the person carrying the detonator for a bomb planted on the fire escape.

Chapter 8
Release Date: 31 March 2009 and 3 April 2009
Rachel realizes the commander must be the one planning to detonate the bomb. She follows B squad into position, then assaults her commander and takes the detonator from him. Meanwhile, a truck has pulled up to the building, and the fugitives try to get to it while ducking gunfire. Rachel teleports herself and the commander into the sky, and sets off the bomb while teleporting herself back next to the truck. With the other agents killed or in shock, the fugitives board the truck with Rachel and flee the scene. Later, while riding in the truck, Anna gets a message from REBEL and Rachel is summoned by Danko.

Chapter 9
Release Date: 7 and 10 April 2009
Rachel reports to Danko's Building 26 office. Danko, not acting himself, interrupts Dan's interrogation. Back on the highway, Rachel is contacted by Rebel once again. Meanwhile, Anna heads to a circus, following Rebel's instructions. She locates her contact, a magician who is also the ringmaster of the circus, but he doesn't believe her at first. Anna follows the ringmaster into a dark back tent and learns that government is after everyone else but the ringmaster, and he is the only person there without an ability. She tries to get everyone to leave, but they decide to wait for someone else.

Chapter 10
Release Date: 14 and 17 April 2009
Rachel rescues two fugitives from Building 26. Anna learns the identities of LAWR and the true meaning of "Ellen". The next morning, Rachel arrives at the circus lot, and passes through the aftermath of a battle that was waged the night before. She approaches a gathering of agents who are questioning a prisoner. Rachel turns to search for the circus group's hiding place, but the prisoner spots Rachel and calls out to her for help. Rachel tries to teleport away, but is captured by Janey Pierce.

Chapter 11
Release Date: 21 and 24 April 2009
The battle at the circus is over and the heroes have been captured by the government. Rachel is forced to make a life altering deal with Danko while Janey Pierce still longs for vengeance. Ricardo Silva returns to save Anna but Janey uses him for her own plans. When Anna awakens, she and Ricardo rush to the Ellen warehouse to try and stop Rachel from completing her mission of killing Linda Niles. Rachel meets with Linda and realizes the unthinkable truth, Linda is in fact Leona Mills, her mother. Leona makes a run for it and ends her own life to spare Rachel the task of doing it herself.

Chapter 12
Release Date: 28 April and 1 May 2009
Leona Mills is dead and Janey Pierce has arrived. In the heart-pounding conclusion to "The Agent", Rachel and Janey face off in a fight that could mean the end for one of them. Just as things seem worse, other heroes such as Abe and Howie step into the fight and together, the specials defeat Janey. But one more question remains: What happened to Leona? Having faked her death, Leona meets with Angela Petrelli and the elusive Micah Sanders. Micah does one more favour for the troubled leader of Ellen and finally reunites mother and daughter.