Pride is killed by Technos early on in the series, leaving a devastated Salene behind. Many characters leave the city frequently, mostly going to the shantytown, Liberty. When Java attempts to kill Ebony, she kills Siva instead. Ebony kills Java in revenge. Lex, once again faced with the loss of another loved one, finds himself the object of the much younger Gel's attraction.
As the series develops we discover that the Zootists are a ploy by the new Techno leader to regain control of the city. He plays a vicious game by publicly demonizing this tribe and advocating the need for a safe zone, fenced-off with secure exit and entrance points. He gradually extends the safe zone to gain a stronger control of the city.
In Liberty, a resistance with the goal of taking the tyrannic city leader down is set up. The overthrow is successful; however, even though the Mall Rats are back in control, there are things happening beyond their reach. The Technos had developed several projects that now spin out of control: the creation of an Artificial Intelligence (AI) and a new virus. The AI develops too quickly and comes to the inevitable conclusion that human beings are a threat to the world. Its attempt to eliminate humankind is prevented, but not before a generator next to the virus-container goes critical. The Mall Rats inform the rest of the city in the hopes that people will evacuate themselves before the generator blows up, thereby releasing the virus.
The entire series ends on a triumphant but sorrowful note. The Mall Rats manage to escape the city by sea, but are sad to be leaving the home they've known for so long behind. The ending shots show the longest-running characters, Amber, Ebony, Lex, Ellie, Trudy, Salene and Jack, along with Jay and Slade, standing at the back of the boat, casting their final glances at the city as they leave it behind for an unknown future.