Max invites Logan to a dinner at her place but instead of having a good time together, Logan is set on investigating a suspicious transportation of what he thinks is medical supply. Max begrudging agrees to help him survey the scene. Later, Logan is captured by the very person he is pursuing and kidnapped. He is demanded to give up the identity of Eyes-Only just as Max impersonates him on TV, saving him in the process. Back at Jam Pony, Normal has a date with a woman who is actually transgender. After he finds out, he decides that he doesn't care about her past, only ...
Logan asks Max to keep a vital witness to a case for 24 hours, which turns out to be a very long 24 hours for Max. What they did not know is that this witness is the reason Logan is in his wheelchair. Killers are sent in to kill the witness and Max is able to overcome them. However, a second set of killers show up. They are unusually strong and their target is Max.
Logan asks Max to be his date for a cousin's wedding where she meets his snobbish uncle and aunt. She also gets to meet Logan's ex-fiancée. Back at Jam Pony, Normal is taken by the mob when there is a delivery mix-up. Original Cindy and Max decide to help him retrieve the right painting to save their boss' life.
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.
Zack manages to escape from Manticore and calls Max comes to his rescue. What they do not know is that this is planned by Lydecker in an attempt to find the escaped X5's. Once Max and Zack find this out, they have to find a way to warn their siblings without exposing them.
Logan Cale's legs are failing him and he secretly contacts an ex-Manticore scientist in an attempt to get back on his feet. He tries to avoid the suspicious Max from knowing. Max's curiosity leads her to follow Logan on one of his trips when she is attacked by Jace, one of her X5's siblings who refused to escape.
Max and Logan are out for a holiday. Unbeknownst to Max, Logan is also planning to investigate an old crime. Once there, Max befriends a small boy with a secret. Stirring his past brings troubles from the town's gangster to Logan and Max. Meanwhile, a powerful seizure takes over Max.
A body with a barcode tattooed at the neck is sent to the morgue. Logan pulls some strings and Max gets to examine the body. Although the barcode matches that of Ben, one of the 12 escapees, the man is not an X5. More bodies with the same tattoo surface and Max is determine to find Ben to find out the truth.
A suspicious-looking man takes pictures of Max. She follows him and is surprised that he seems to possess super-natural strength. Finding out that he is actually a good guy, the two team up with Logan and investigate the deaths of recently released prisoners. This leads to shocking discoveries about Logan's family business. Logan is left with a dilemma. If Eyes Only goes public about this finding, he would lose his source of income.
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.
Max is in heat again, ready to jump at any men, even Normal! She hates her condition and is ashamed of it. Meanwhile, she is avoiding Logan at all cost and decides to cancel their anniversary dinner. After the day is over, she confronts the still-confused Logan about her condition and the two finally admit their feelings towards each other. Just as they are kissing, Zack interrupts with bad news about Tinga. They must go rescue her from a secret government facility.
Lydecker realizes that he has lost control over Manticore, as Madame X is now clearly running the show. He would rather see the project destroyed than see it abused by others. He asks Max for help in bringing Manticore down. Together with Zack and other X5's, they storm the facility and destroy the DNA lab.
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.