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.

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.

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.

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.

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.

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.

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 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.

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.

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.

Max and Logan look for Joshua, who is wandering Seattle looking for "Father", the man who created him. Meanwhile, Alec fights ordinary people in an underground club but when later caught by White, he must strike a bargain to kill three transgenics to save his life.

Max must break her vow to avoid Logan after Joshua's friendship with the blind woman makes him a target of a transgenic manhunt in the sewers. Meanwhile, White leaks news of the human-looking X-5s to the media, leading to a wide-scale attack against the so-called "monsters" running amok and to the death of a someone dear to one of the transgenics.

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.

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.

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 discovers that Zack is not only alive but apparently benefiting from some cybernetic enhancements to his genetic engineering, however he does have memory problems. Knowing that Zack sacrificed his life for hers, Max puts herself at great risk, attempting to rescue him from his new "owners," a vicious Seattle gang but when an attempt is made on Logan's life, Max is faced with a very painful decision.

Max and Logan find themselves caught up in a spellbinding kidnapping case, that takes surprising turns when they learn the boy is the son of the infamous Mr. White. White, upon learning of Max's quest to find his son, decides to turn the tables and capture her instead and Max must race against time to save the boy, herself and discover the truth behind White's identity.

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 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.