The episode begins when a boy is taken from his bedroom, and the perpetrator leaves behind a white chrysanthemum on the boy's bed. Soto is listening in on a police scanner while drawing comics of his exploits with Hansen, and he recognizes the details of the kidnapping as the MO of one of the '63s, Kit Nelson. If the pattern holds, the boy will be returned home soon, but he will be dead.
Back in the past, Nelson has been sent to Alcatraz for the kidnapping and murder of young boys. Child killers are looked down upon in the prison, and the rest of the inmates gang up on him and pummel him within an inch of his life. Whilerecuperatingin the prison hospital, Nelson is treated by Dr. Beauregard, who only gives him the barest of care, because he's a father himself. Also, Nelson has a talk with Rebecca's grandfather, who is still in the infirmary.
Madsen and Soto speak with the kidnapped boy's mother, and she confirms what Soto has suspected about the details involving the case. Suddenly, Hauser arrives and calls off the Amber Alert for Dylan, not wanting any more publicity drawn to the case. Soto is livid, thinking that Hauser has just signed the boy's death warrant.
As Nelson takes the boy on some mundane activities which seem to have some significance for him (fishing and watching movies), the flashback to the past shows Nelson speaking with his father in the visitors' area. His father asks him whether he'd killed his brother, but Nelson denies it, saying that the boy died of scarlet fever. Dad Nelson doesn't believe it, and is glad that his son is going to rot in prison.
Soto follows Nelson's patterns and, knowing that he'll take his victims to eat cherry pie, seeks out diners which sell it. He notices Nelson and Dylan in a booth nearby. He calls Madsen and tells her that he knows where Nelson and Dylan are. Soto then tries to stall Nelson without raising his suspicions, but it's no use. Madsen arrives, weapon drawn, but Nelson aims his own gun at Dylan's head. He manages to escape, but not before Soto tells Dylan not to give up.
Back at past Alcatraz, Warden James gets Nelson into solitary for an impromptu interrogation session. The two men are in a small, dark cell, and the warden lights a match, saying that they're going to have a four match conversation. He asks Nelson about what really happened to his brother. Nelson must tell the truth before he runs out of matches, else he'll be stuck in solitary for his entire sentence. Nelson eventually admits to murdering his brother, because he was jealous of his mother's affection for him. The chrysanthemum was used because it was his mother's favorite flower. He realized, then, that he enjoyed killing little boys.
Soto figures out a possible place that Nelson might have taken Dylan, a bomb shelter located out in the woods. Dylan manages to escape the shelter, but Nelson gives chase. Soto and Madsen arrive and again Madsen draws her weapon. Nelson taunts her, saying that she doesn't have the guts to shoot. Nelson gets shot in the head by Hauser, and Dylan is safe.
Hauser berates Soto's actions on the case, and reminds him that if he didn't know so much about the inmates of Alcatraz, he'd let him go. Soto returns to Dylan's house, giving him some rare comics and confiding in him. He says that he was also kidnapped as a boy, and that he escaped, but it wasn't easy. He tells Dylan that surviving something like this gives you a superpower.
Hauser brings in Nelson's dead body into the new prison, where Dr.Beauregard(not aged since the '60s) is set to perform an autopsy.