Lydecker gets the local police to post "Wanted" posters of Max throughout the city, charging her with Vogelsang's murder. When Zack returns to beg Max to leave town, Logan offers both of them shelter in a countryside retreat. Meanwhile, Sketchy is put in charge at Jam Pony and Normal goes to the police about Max.

A group of South African known as the Red Series is after Max's DNA in an attempt to improve their enhanced soldier. They take Original Cindy hostage to lure Max out. The rescue reveals Max's true identity to her best friend.

Tinga, who escaped to Canada in #1.12 with other X5's, when Eyes Only warned them their locations were compromised, comes back in town to save her husband and son. With Max and Zack's help, the family is reunited, but not before the son is given a deadly pathogen. Lydecker agrees to cure the boy in exchange for Tinga. Unbeknownst to him, Madame X has already arranged for Brin to double cross Lydecker. She captures Tinga, who is able to pass her special traits to her children, to study her.

After months of being imprisoned at Manticore, Max has resisted powerful attempts at re-programming and breeding and plans her escape from the genetics lab. She is aided in her breakout by the gentle but beast-like Joshua, an early Manticore creation, and together they release all the other Manticore creatures. Max attempts to reunite with Logan, only to discover that he is now number one on Manticore's most wanted list.

On Halloween night, Max finds her "normal" world turned upside down when the creatures she let out of Manticore are able to walk the streets freely without fear of exposure. As she and Joshua, with a crazy band of characters, race against time to find a headless body before it carries out its intended lethal mission, Max is faced with the reality that Asha and Logan are getting closer than ever.

While being haunted by music from the past, Alec must revisit one of his Manticore missions that went bad and resulted in the loss of his one true love. Max attempts to put the pieces of Alec's past together and upon discovery of the truth sets out to help him as best she can.

Max and Logan track Ames' kidnapped son, Ray, to a small town where the breeding cult known as the Familiars, are readying their youngest creation for a mysterious ceremony.

Max begins to develop strange markings on her body while leading a transgenic resistance against White, when he attempts to capture one of her "brothers". However, the transgenics are stunned by revealed secrets about their "father" that threaten all that they believe and stir up many more questions. Meanwhile, the Terminal City dwellers mount a campaign to battle the humans hunting them down, and Alec learns why Logan has been keeping his distance from his former friends.