Max regains her consciousness after her heart transplant, only to realize that she is back at Manticore and that Zack's heart is beating inside her. Madame X or Dr. Renfroe brings her to what is remain of Zack, his various organs taken to save other X5s. Now that the DNA lab has been torched, Manticore has decided to designate a 'breeding partner' to every X5's. Max's turns out to be Alec, a clone of Ben, who has no problem with her refusal to 'mate' with him. With the help of Joshua, a half dog- half man experiment, she escapes from Manticore for the second time. ...
The government sends Ames White to clean up the mess that was Manticore. His mission is to eliminate all evidence of the program's existence. Max feels guilty about this, as she was the one that let the X-series out, and goes back near the facility to help a group of escapees evade death. Lydecker contacts Logan to warn Max to stay away from Manticore when he gets her full DNA analysis.
Alec agrees to kill three Manticore escapees when White plants a small bomb at the back of his head. He must bring their barcode back as proof. When time begins to run out, he contemplates attacking Joshua and Max to save his life. Logan agrees to pay a huge sum to the man who engineered the virus designed to kill him to find an antibody for Max.
Max and Logan are separated by the virus. Their loneliness compels them to date other people. Meanwhile, a virus is on the rampage in Chinatown. Because there is a rumored transgenic in the area, the public starts to believe that this monster is the source of the illness. In reality, White has asked a scientist to engineer a virus targeted specifically at Manticore's escapees. The death in Chinatown was just a demonstration for White.
It's Halloween. Joshua, seeing people dressed up as monsters, believes it the perfect night for him to experience the outside world. He asks Max but she decides against it, insisting that people will be scared of him. Joshua reluctantly agrees to stay inside while Max prepares to go to a party.
A canine-like creature has been attacking and killing police. All evidence points to Joshua. Max refuses to believe that someone as gentle as her friend can kill. It turns out that Joshua has a younger brother called Isaac. The police tracks Joshua down and arrests him. Max breaks her friend out of jail. To protect Max, Joshua kills his brother. Meanwhile Alec is selling drugs, using his position as a Jam Pony messenger as cover. The local gang comes to threaten Alec into stopping to sell drugs in their territory.
Max is surprised to find that Zack is still alive, working for a gang. He has no recollection of his past life. Once he starts regaining his memories, he only remembers that Logan stole Max from him and that Logan is the reason Max was captured by Manticore. He is out to get revenge on Logan. Max has to choose risking Logan's life or losing her brother to another memory loss.
Logan and Max become involve in a kidnapping of a young boy when his distressed mother came asking for help. During their investigation, they learn that the boy is the son of Max's nemesis, Ames White. He is part of a breeding cult and has placed his only son in a special school without his wife's knowledge or consent. The boy's life is in danger as he must pass series of deadly tests to prove his worthiness to the occult group.
When Asha's militant group, S1W comes under fire, Max discovers that it is all because of a Manticore strategist - another transgenic called Brain. Although Max doesn't trust him completely, Brain sets out to protect Max in the best way he can as they discover who really betrayed S1W.
The past catches up with Alec who is sent on a package delivery run to a residence with Max. Before he escaped Manticore, he was being groomed as an assassin. On just such a mission, he brought immense sorrow to the owner of this residence--The Berrifords. Having no idea what inner turmoil is driving her erstwhile Manticore nemesis/friend, Max nonetheless is able to help him face his demons and resolve the sins of his past--the wrongs that he could never quite escape, the haunted feelings that were never very far away.
Max and Logan finally find a cure for the genetically engineered virus created by Manticore which only endangers Logan when he has any form of physical contact with Max. However the cure is temporary and lasts only ten hours and fifteen minutes . Meanwhile Seattle is being besieged by a Manticore creation which is preying on humans and it is left to Max to try to save the day.
Max is rushed to the emergency room after she gets shot trying to protect a little boy. While there, blood and DNA tests expose the virus inside of her. The CDC is contacted, Ames White catches wind of it, and it's a race against the clock for Logan to help Max escape.
A transgenic with the ability to control people messes with Max's mind to keep her from coercing a meek mob bookie into selling out his boss to Eyes Only. But once the mutant sets her sights on Alec, the stakes are raised, leading him back into the boxing ring to make some money for some not-so-good fellas.
After nearly infecting Logan, Max decides to end their affair for good; Alec's haunted by the sins of his Manticore twin; also Aimes White triggers a witch hunt by leaking information about the Manticore transgenics.