Lydecker gets the local police to post ""Wanted"" posters of Max throughout the city, charging her with Vogelsang's murder. Zack returns to beg Max to leave town. Logan offers Max and Zack shelter in a countryside retreat. While saying good-bye, their attraction to each other comes to the surface and Logan and Max kiss. Zack tries again to convince Max to run away with him. Just as she's ready to do it, she learns Logan is near death. Max heads back to Seattle to give Logan a blood transfusion. Though she puts her own life at risk, she does save Logan's life. Lydecker and the police close in on finding Max; however, the real murder confesses. It's Zack who turns himself in to police in order to spare Max. The helicopter transporting Zack back to Manticore mysteriously explodes. No one knows if Zack was killed. Meanwhile, Logan discovers the feeling has partially returned to his paralyzed leg. And, Sketchy is put in charge at Jam Pony. He seizes the opportunity to make himself look li

The ""transgenic"" Reds catch up with Max when her lost pager reveals her whereabouts to them. The Reds are former death row convicts seeking to combine their technology with Max's genetic material. Logan and Max, after a deadly fight with a Red, learn that the transgenics' power is controlled by a special implant placed in their bodies. Meanwhile, the Reds take Original Cindy hostage and used to lure Max into their trap. Max risks it all and inserts the Red's implant into her own neck in hopes of gaining extra power. The implant makes her hyper violent and she kills off the Reds in order to free Original Cindy. Max then has a seizure. Logan learns the only way to save Max's life is to get the chip out of her head, but first he has to electrocute the chip in her neck. He is able to save her. Max then has to reveal to Original Cindy her Manticore secret. Also, Logan begins to regain the use of his legs and stands up.

When fellow X5 escapee Tinga returns to town to save the family she left behind, Max, with the help of Zack, once again places herself in danger to battle Manticore, Lydecker, newly turned X5 Bryn, and an increasingly power-hungry Madame X. When Tinga gives up her freedom to ensure her child's safety, she is taken to a secret government lab. Amid the double crossing, we learn Lydecker is no longer in the loop with the real Manticore higher-ups. This means Max is in more danger that she could possible imagine.

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.