Zeta and Roe are rescued from Bennett by three hackers who claim to be Internet hacker types who want to free technology for the people. They're sort of right: however, they plan to dissect Zeta to find out how he ticks, while one of their members, obsessed fan Buss, keeps Roe prisoner. Roe and Zeta both manage to escape, but Bennett arrives. In the subsequent pursuit, Buss rescues Roe but Zeta is captured and taken in by Bennett in preparation for a complete CPU wipe. (to be continued)

Agent Bennett still believes that the captured Zeta has been programmed to believe he is acting of his own volition, a suspicion that seems to be borne out when the research team discovers a previously unknown chip in Zeta's head. Roe plans a rescue but it goes amiss when Zeta protects his memories from removal by transferring them from sector to sector. This results in the activation of his old killer-type programming. He goes on a rampage but Roe manages to get through to him and they manage to escape the NSA compound.

The parts from the IR hunter unit, that were destroyed by Zeta in a hospital, find their way into the hands of a young boy who likes to build things. The boy, Jace, accidentally activates the primary chip and the IR unit proceeds to rebuild itself from scratch. Zeta gets wind of the unit's activation when he notices the shipment of parts under the unit's ID. Tracking it to Jace's house, Zeta and Roe end up fighting the unit, and with Jace's help Zeta removes the primary chip and deactivates the unit.

Zeta and Roe are on the trail of one of Selig's associates, who is in a business/administrative area, the Hub. However, it's a trap set by Dr. Boyle, who attached a credit-nullifier to Zeta. In return for removing it, the two must steal items for Boyle for his research. Further complicating matters are Agents West and Rush trying to track them down. Eventually Zeta and Roe manage to lose the agents and set up Boyle to remove the nullifier and then be spotted by the NSA agents, while making their escape.

The Brain Trust kidnaps Ro to force her into helping them setting off radioactive waves that would bring out children's psychic powers.

Zeta malfunctions and recovers his memory of the moment he decided not to hurt people, when he is ordered to impersonate Eugene Dolan but instead gets close to him and his family.

Forced to take refuge from a tornado, Ro and Zeta meet two brothers, Dex and Carl, who are using an experimental process to disrupt tornados. They partially succeed, and the two fugitives join up with to get moving when their car is destroyed. With Zeta's input Carl the smart one manages to come up with a complete process, but pilot Dex gets the glory. Carl goes off on his own to take on another tornado and gets in over his head. With Zeta and Ro's help Dex rescues his brother and the two settle their differences.

Bennett tracks Selig via highly secure files to a research base where Selig was studying aquatic regeneration. Ro and Zeta are also there on the trail of Zelig. Bennett takes his son James Jr. along and while Ro, a local boy and James go underwater in a sub, Agent Bennett spots and pursues Zeta. But the kids get in an accident. Zeta reveals himself and volunteers to go down and Agent Bennett goes with him. Zeta has to act as the rudder for the injured sub to get everyone to the surface in time. At the end Bennett has to choose his son over capturing Zeta.

Ro and Zee take refuge at a ""Pictocon"" - basically a 21st century comicbook con where they take on the role of Owl Man and Squirrel Girl. Bucky contacts them there and puts Ro in contact with her long-lost brother Casey MacCurdy, a reporter. Casey's boss Jenson finds out he is the brother of a renegade and first insists he do a story on it, then alerts Bennett and the NSA. Ro and Zee duck the NSA in San Francisco but Casey sets up another rendezvous on the Golden Gate Bridge. He's persuaded to make it a trap. The NSA close in but Casey sides with his sister and helps them to escape. Casey plants an ad with a secret message for Ro reassuring her, but is under NSA scrutiny so their family reunion is delayed...but Casey starts to get the true story out on Zeta.

The NAS find out about Bucky and make plans to capture him and, through him, Zeta and Ro.

Zeta's quest to locate Dr. Selig leads him to another member of the infiltration unit design team, Dr. Myrell. He runs a non-profit organization called the Myrell center, where he constructs and tests new technology to help the handicapped. One of these is a young man named Kevin, who is confined to a wheelchair. The doctor has created a backpack device called a ""synaptic amplifier," which allows him to walk normally. Zeta and Ro sneak into the center disguised as Kevin and his backpack, but end up encountering a thief there to steal the real amplifier pack. On a non-handicapped person the pack provides them with fantastic strength and agility. Blake, the thief, escapes, but a security guard who had seen the Zeta/Ro illusion of Kevin there after-hours accuses him of the theft, and he is arrested for it. It's up to Zeta and Ro to find Blake and clear the innocent Kevin.

Zeta and Ro are on the run from the NSA when they stumble into a No-Tech community. The group is protected by law so Bennett can't go into their community without a local warrant. Zeta and Ro take refuge there but Zeta's robotic nature is soon discovered by Amy. She advises them to keep Zeta's nature a secret. Zeta predicts the No-Tech's river levee will break during an upcoming storm. Bennett gets his warrant when the No-Techs use a catapult on West. Zeta has to reveal his true nature to save the No-Techs and is damaged. The No-Techs take Zeta prisoner and prepare to destroy him but the levee breaks. Zeta rescues the No-Techs and they come to appreciate his non-soulless nature as the two make their escape once more.

Zeta and Ro break into an NSA depot used to store holograms/robots. They spot Professor Zelig, who downloads information and leaves. The two follow him to a steel yard where he is revealed to be Professor Edmunds, who worked on Zeta's hologram projectors. He is being blackmailed by Sweet, the head of Brother's Day, an anti-tech terrorist organization. They get Edmunds to work with them to lead them to Selig, unaware that Brother's Day has followed them to the hologrammatically concealed floating fortress where Zeta's creator is working to create semi-organic synthoids. Sweet plants an explosive as a disguised Zeta confronts his creator who confesses he secretly planted a "conscience chip" in Zeta (which Bennett overhears). Sweet triggers the explosion before Zeta can reveal who he is. Sweet shoots the escape pod with Selig as he escapes and the scientist is believed dead.