The story's main character, Infiltration Unit Zeta, is a humanoid robot (synthoid) designed to carry out covert assassinations on the behalf of the National Security Agency. However, when Zeta discovers that one of his targets is innocent, he experiences a kind of existential crisis about goodness and the value of life; following this epiphany, Zeta finds he can no longer kill. The newly enlightened Zeta refuses to continue on as an infiltration unit and abandons his mission, going rogue. Zeta is pursued by a team of NSA agents, led by the obsessed Agent Bennett, and is aided by a 15-year-old runaway, Rosalie "Ro" Rowan.
The Zeta Project follows the exploits of Zeta and Ro as they attempt to prove that he is genuinely non-violent, whereas the NSA agents pursuing him believe that the terrorists he was investigating before going rogue have reprogrammed him for some unknown purpose. To prove his innocence, Zeta and Ro search for his creator, the elusive Dr. Selig.
Infiltration Unit Zeta (Diedrich Bader), nicknamed "Z", the titular character. As an infiltration unit designed to seek and destroy specific people, Zeta has the ability to holographically disguise himself as any individual he has seen, as well as create custom appearances through mixing and matching various physical traits. Though Zeta no longer possesses the vast array of weapons he originally came equipped with, his arms are equipped with saw blades and cutting lasers. He also possesses a wide array of other non-lethal tools such as handheld welding lasers and a computer interface. In addition, Zeta possesses great mechanical strength, has extensible limbs, and is capable of self-repair.
Rosalie "Ro" Rowan (Julie Nathanson), a 15-year-old orphan who joined Zeta in his quest to prove his innocence. She usually acts as a wiser older sister to Zeta, who is often clueless about how to properly blend in with humans. She sees Zeta as family, and refuses to abandon him since she owes him her life. In one episode, it is revealed to Ro that she has a brother.
Infiltration Unit 7, a later model of infiltration unit who Zeta comes into conflict with after foiling one of his missions. Infiltration Unit 7 possesses all of Zeta's abilities, greater strength and durability, and a much larger arsenal. It is much less subtle in the execution of its duties than Zeta, and hence, from Zeta's viewpoint, it is evil.
Agent James Bennet (Kurtwood Smith), the leader of the NSA team sent to capture Zeta. He vehemently believes that, regardless of Zeta's behavior, there is some sinister motive behind Zeta's sudden change in attitude and believes he is working with the terrorist organization Brother's Day.
Agent West (Michael Rosenbaum), a young, arrogant and egotistical agent whose desire to prove himself only results in annoying his superiors, coworkers, and virtually anyone else he meets to the point that Ro no longer even considers him a threat. He shares a last name and is similar in appearance to Wally West, the only Flash in the DCAU. Both characters are also voiced by Michael Rosenbaum.
Agent Lee (Lauren Tom), a compassionate female agent who comes to see Zeta in a more redeeming light as he continues to go out of his way to help people. She later quits the team; later episodes imply that she was subsequently promoted, and is now able to occasionally help Zeta escape from the people she worked for.
On March 17, 2009, Warner Home Video released the first season on DVD in Region 1. This release has been discontinued and is now out of print.
On March 14, 2017, Warner Archive will release season 2 on DVD in Region 1 for the very first time. They will also re-release the first season on the same day. These are Manufacture-on-Demand (MOD) releases, available exclusively from Warner's online store and Amazon.com.