The story's main character, Infiltration Unit Zeta, is a government robot designed to destroy and (via holographic projections) impersonate targeted individuals. However, while observing a target. Zeta experiences a kind of existential crisis about goodness and the value of life; following this epiphany Zeta finds it can no longer kill. The newly enlightened Zeta refuses to continue on as an infiltration unit and abandons its government service.

Zeta is pursued by a team of NSA agents, led by the obsessed Agent Bennett, and including Agent Lee, Agent West, and Agent Rush. On the way, he meets up with a 15-year-old runaway, Ro Rowen. Together, they search for Zeta's creator, the elusive Dr. Selig, in an attempt to prove Zeta's sentience and earn him his freedom.

The show was created by Robert Goodman, and starred Diedrich Bader, Julie Nathanson, Kurtwood Smith, Dominique Jennings, Eli Marienthal, Scott Marquette, Michael Rosenbaum, and Lauren Tom.

Both Batman Beyond and The Zeta Project crossed over with each other in certain episodes. The Zeta Project ran for two seasons, and last aired in August 2002. Like Batman Beyond, the series ended without a conclusion. There was never a release for the remaining story and so Zeta and Ro's quest for personal answers were never answered and are up to viewer interpretation.

The training robots used by the animated Justice League (which shares DC animated universe continuity with The Zeta Project) are very similar to Zeta's first appearance in Batman Beyond, establishing that the robots were initially developed decades before Ro met Zeta. One of these robots was used by the government to attack Supergirl in the Justice League Unlimited episode "Fearful Symmetry", where he was noted to be a "Z8" type.

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