Lydecker realises 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 is forced to expose her true identity to the world, when she must defend her own kind during a potentially deadly hostage situation at Jam Pony, involving Joshua and Alec.

Tired of Logan's "all business" approach to their relationship, Max refuses to help with his latest case involving a medical supply smuggler. But when Logan gets double-crossed by his target, Max goes undercover as "Eyes Only" to rescue him from a certain death. Meanwhile, Normal is smitten with a woman with a secret.

Max needs her pills to keep her seizures at bay but her friends believe that she's an addict. Max is feeling the serious side effects from the alterations to her biochemistry. After her friends flush her pills she tries to steal some from the local hospital but get's caught and lands up in jail.

In a post apocalyptic world genetically enhanced female (transgenic) Max Gueverra tries to stay ahead of the law while looking for links to her past. Max does a job for Logan (the last good man on Earth; and cyber journalist Eyes Only) while trying to keep a handle on her revved up hormones, thanks to Manticore. Logan manages to turn up some information on a friend from Max's past.

Zack reappears and tells Max Lydecker has captured Brin, one of their Manticore sisters, and plans to do her harm. Max decides they must kidnap Lydecker and force him to reveal Brin's whereabouts. When Max and Zack discover that Lydecker was not behind Brin's disappearance, they have no choice but to team up with Lydecker to find their lost sister.

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.

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.

Manticore sends out a signal ordering all the escapees to return to a site where unbeknownst to them, awaits their death. While harboring a group of muddle Manticore escapees, Max is captured by a man who job it is to exterminate the remaining fugitives, leaving only Alec and the X6's to rescue her. Meanwhile, Lydecker contacts Logan when he gains information about Max that could be dangerous if it falls into the wrong hands.

A genetically enhanced hypnotist targets Logan and Max, who reveals her true identity and Logan's secret activities before realizing that she is being manipulated as part of a deadly plan - but luckily she doesn't remember doing it. Meanwhile, the transgenic, Mia, also sets her sights on Alec, raising the stakes, leading him back into the boxing ring to make some money for some not-so-good fellas.

After a near-fatal incident with Logan, Max decides to end their relationship for good. A murder committed by Alec's Manticore twin, Ben, puts him under suspicion and places all of the transgenics in jeopardy...thanks to White and his leakage to the media. Meanwhile, Joshua finds the perfect woman, but can't find the courage to confess his secret.

Max's life is placed in more danger than ever before when she is hunted by the one person who knows her better than anyone -- her clone. Though even the existence of this exact replica is news to Max, she quickly realises the imminent danger from an individual who can get inside her head and infiltrate her life like no one else. Dealing not only with this new threat but also the disintegration of her relationship with Logan and Joshua's disillusionment over not being able to go out in public, Max must race against time to figure out how to stop this deadly enemy before it's too late.

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.

The trouble starts when Logan recruits his favourite biker chick to protect a Federal witness with vital info on local corruption. But the operation hits a snag after Max realises that the guy she's guarding is a face from the not-so-distant - and very painful - past, and that those who want him dead may have plans for her as well.

12 genetically enhanced children escape from a military base that created them. 10 years later, after The Pulse, a magnetic bomb that destroyed every computer in USA, has struck, Max Guevara, one of the 12 escapees, is a bike messenger in (what's left of) Seattle and with cyber journalist, Logan Cale, she tries to rid the world of crime and corruption, avoid her creators and uncover her past.

Max and Donald Lydecker are taken hostages at a convention. Logan decides to trade himself as a hostage for all the women. Max decides to stay and ends up helping Logan when the terrorists push him off the roof of the building. She also does the unexpected when she saves Lydecker from being shot in the head.

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.

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, she 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.

Max discovers Logan is dealing with a back-alley medical clinic doctor who has agreed to perform experimental therapies to keep him out of his wheelchair, who Max realises is also a former Manticore scientist. Meanwhile, Original Cindy returns to Jam Pony and continues to learn more about Max and her relationship to Logan.

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 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.

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.