Max escapes from Manticore and triggers Operation Pale Face that causes Manticore to self-destruct, in order to cover all trace of its existence.
A clean-up operation begins and all the transgenics that escaped from Manticore are the targets. Max feels responsible and attempts to save them.
Max tracks Joshua to Sandeman’s former residence. Lydecker discovers a secret archeological dig of a Kiloma Indian burial site that is somehow connected to Manticore. Alec is captured and about to be excecuted by White, and Max must save him.
Lonely, and frustrated that they cannot be together, Max and Logan reach out to their friends. Manticore creates a pathogen that can target and kill a specific race of people, aiming to wipe out transgenics.
Max spends a wacky Halloween with other transgenics, chasing a headless body in an attempt to foil an assassination plot.
A creature called a man-dog is killing cops, and Max discovers that one of Joshua’s brothers is behind the attacks; Alec gets hired at Jam Pony, and runs into trouble when his black market business selling synthetic hormone riles local thugs.
Max discovers that her brother Zack is alive and living with a group of Steelheads, but he is not the same Zack as she remembers.
When a group of fisherman find a girl with gills in one of their nets, they believe they’ve caught a mermaid. But Max and Alec soon realize the mermaid is actually another Manticore escapee, and they set out to rescue her.
Eyes Only agrees to help a a woman find her kidnapped son, but Logan and Max are stunned to learn that the woman is Ames White's wife; trouble arises when Alec takes advantage of Joshua's apparent talent as an artist.
After an S1W cell is busted, Max discovers a man named Brainiac who seems able to predict the future.
Alec stumbles across a troubling reminder of his past as a Manticore agent and is haunted by memories of the girl he fell in love with—and killed.
Max finds a temporary cure for the virus that targets Logan; Joshua discovers that a Manticore-made “sniffer” is loose.
Max is shot, and rushed to a hospital, where her blood work reveals some strange anomalies that tip Ames White to her presence.
Max stumbles upon a group of apparent transgenics who survive by drinking their leader’s blood. Alec covertly assigns Joshua to make deliveries for him.
When Logan asks Max to help him get a mob accountant to become a police informant, she runs into a fellow Manticore alum with unusual powers.
After Logan traces a call, he and Max find Ames White's son, Ray, in a mysterious school.
Logan touches Max and nearly dies from the virus; Alec is arrested for murder; White discovers the transgenics are immune to his cult’s snake blood, and arranges to have the Manticore experiment exposed.
With Ames White’s help,the news is full of reports on transgenics. When Joshua leaves his house to see Annie, he is spotted, and further chaos erupts.
As their secret identities are revealed, Max, Joshua, and Logan decide to leave town for Terminal city; White captures a transgenic that he thinks is Max, but is actually her clone.
An escapee from an insane asylum infiltrates the transgenic society in Terminal City. White’s operatives discover a way to identify transgenics in a crowd.
After Max and other transgenics are surrounded by police in Jam Pony, White brings in a special team sent by the Breeding Cult, intending to kill Max and all the others.