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.

Alina Herrero contacts Eyes Only and asks him to help her find out the truth about her father's disappearance years ago. Max breaks in to the police department to steal information about her father, who also happens to be Logan's mentor. At the same time, Sketchy loses the mob's money and has to return the full amount in 36 hours. Max uses her super skills to win the money through poker.

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.

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.

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.

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.