Picking up where the "season finale" left off, Emily and Susan are on life support after being contaminated with a virus, which is found to be from a Purist group. The Purists have created a mass of it to spray over LA to kill all Newcomers. At the same time, an elite Overseer arrives to organize the return of the Tenctonese to slavery, and decides to take the human population as well.

Sikes and Francisco are called in to a case when a mysterious young girl, who looks part Newcomer, part human, appears. Her huge, brutish counterpart tries to free her from the precinct, and their bizarre relationship turns out to be the result of a slaveship medical experiment. Meanwhile, Cathy and Matt are going to sex school, in preparation of becoming intimate, while Buck distresses his parents by his anti-human opinions.

It's 1999, and as the end of the millenium approaches, people are attempting to find spiritual enlightenment. But a few people want to skip all the work that entails, and a holy Tenktonese relic in the hands of a heretic is giving them a shortcut. But it's not quite as easily controlled as she says.

When detectives Sikes and Francisco is presented with the mysterious death of an Eeno, Matt is stupefied to discover that George rudely snubs the case. He, like most newcomers, reviles the outcast Eenos. As the case unfolds, George has to reassess his prejudices, and George's family help save the city from an alien threat originating in an Eeno waste disposal facility.

Matt and George investigate a series of strange occurences involving newcomers, who are found to be programmed to carry out someone's dirty work. The method by which they are brainwashed dates back to the slave ship's rebellion group, the Udara, who we find Susan is a part of. Susan and George's lives are further disrupted when Buck enrolls in the police academy.