Due to the power surge that Mary and Otto caused in bringing Pritchard back to life, two notorious murderers escape from prison. Still determined that this is his city to protect, Pritchard goes on the hunt for them, and Mary - who believes she's partially responsible for the fugitives' escape - offers assistance. Meanwhile, in order to win Duval's trust, Pritchard tells him they're half-brothers
A case from the past comes back into play as Pritchard and Duval investigate a series of murders involving young prodigies. As the investigation unravels, Duval comes to terms with the possibility that Pritchard could be his father reincarnated. Pritchard manages to become a confidential informant for the FBI.
Mary’s life is in danger when a dead pool predicts her death for the same day as an important Lookinglass product launch. When Pritchard is needed the most, he fails to show up and winds up in the hospital after a near fatal brawl. After Pritchard's hospitalization, Otto begins to find glitches in Pritchard’s code that might not only drastically change Pritchard, but Mary as well.
Pritchard's past comes back to haunt him. 20 years ago, Pritchard covered up a murder committed by a drug lord's girlfriend, who happened to be his confidential informant at the time. Instead of staying on the right side of the law after Pritchard helped her elude the crime, 20 years later she has turned into a major drug dealer (guest star Madchen Amick). So now, Pritchard is determined to set things straight. Meanwhile, Mary's cancer is in remission but she and Otto are at odds over Pritchard, and Otto wants to find a new blood donor for her. Also, Gracie starts dating an older guy.
Pritchard and Duval join forces to track down a serial killer, and Alexa and Connor try to procure key technology from Lookinglass. Meanwhile, the bond between Mary and Pritchard has grown stronger, but Otto goes to great lengths to make sure Mary never leaves him, and Gracie suspects there is more to Pritchard than what he has told her.
Pritchard and Duval continue to investigate who Albert Lin really is, who created him and try to uncover how he is involved in a string of murders. The investigation drives a wedge between Mary and Otto, and Otto must choose if he will betray Mary and undo everything they have built, including Pritchard to align himself with Connor Graff. Meanwhile, Gracie goes missing and Pritchard and Duval must race against the clock to rescue her before Pritchard’s time runs out.
Pritchard and Duval race against the clock to save Gracie from Connor and Otto's life-threatening experiment. But time is quickly running out for Pritchard, as well, since there is no tank in which he can regenerate. Meanwhile, Mary, with the help of Alexa, does everything she can to try and unlock the code to save Pritchard's life before it's too late, and Otto wrestles with his conscience and the decisions he's made that have changed lives forever