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.

A mermaid is caught by fishermen and is immediately sold to a night club in Seattle. Max and Alec are intent on returning her to the sea before White and his crew get their hands on her.

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 comes under fire, Max figures that it's all because of a Manticore-engineered military strategist, another transgenic called Brain. Brain sets out to protect Max as best he can, after he's called upon to discover who really betrayed the group.

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.

When Max and Logan finally find a cure for their genetically engineered virus, it turns out to be only temporary. Their time together is limited and to make matters worse they have to stop a strange Manticore creation that is on the loose in Seattle and preying on people.

After Max is shot and hospitalized, Logan must intercept White and a very curious CDC doctor in order to keep Max's transgenic identity undercover.

Max must take on a cult of superhuman-blood addicts when she learns they're being led by a Manticore mutant intent on rebuilding an X-5 army. Meanwhile, Joshua falls in with the wrong crowd after Alec tricks him into delivering his packages for Jam Pony.

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.

Logan and Max track Aimes' kidnapped son to a small town where the breeding cult is readying Manticore's youngest creations for a mysterious ceremony.

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.

Max must break her vow to avoid Logan after Joshua becomes a target of transgenic manhunt in the sewers. Ames White leaks news of the human-looking X-5's to the media.

Max's escape from Seattle is derailed after White sends in her clone to capture the elusive X5-452. Logan's Eyes Only compound is attacked.

Ancient writings appear on Max's skin, while White's brother escapes from the cult and the transgenics gather in Terminal City.

Max and Alec are forced to expose their true identity to the world when they are caught in a hostage situation at Jam Pony.