The scene opens with Emerson walking into a bar. Ray has called him. Ray tells him that he wants Rebecca out and Emerson tells him that he is not the one keeping her in. Ray tells Emerson that Rebecca deserves a real life. Emerson disagrees with Ray’s idea of a “real” life. Emerson tells Ray that Rebecca has the gut Ray never had. Ray tells him that she is his only family and he does not want her to continue being in the task force. Emerson tells him that she is being with the force for months and why does Ray suddenly want her to quit. He thinks that Ray has seen Tommy Madsen and hence his fear for Rebecca. Next, we see two men driving back home. Its dark and the man who is driving suddenly sees someone on the road. He swerves the car and stops at the side.
He thinks he has hit him. When they get down to check, a man with a shot gun shoots one of them and kidnaps the other. Sonny Burnett has resurfaced. We are then taken to the flashback, where our inmate Sonny Burnett, has finished his period of solitary confinement and is due to enter the jungle. He goes to an inmate named Hicks, asking him for protection. Hicks has heard about Sonny. He knows that Sonny was involved in a kidnapping and was paid. Sonny tells him that he is also a businessman and he needs protection as he’s got enemies around. He says that he has still got the money with him and it is safe. The police could only catch him and not the money. Back to the present, Rebecca tells Soto that she keeps having the nightmare about Tommy in her apartment. They arrive at the crime scene. Emerson tells them that the man who was shot is Simon More, 42. Sonny has left his prison jacket behind.
The car is registered in the name of David Pierce and is the CFO of a multimillion dollar company. Soto educates Rebecca about Sonny. He tells her that he ran this like a business but never killed anybody back then. Next, Soto and Rebecca are talking to David’s wife and tell her that this could be a kidnapping and that the kidnapper could ask for a ransom. David’s wife tells them that even she was kidnapped when she was a little girl. And his name was Sonny Burnett. The duo was surprised. Soto tells her that he had never read about her during his research on Sonny. She tells him that the papers didn’t mention her, as she was a minor. Rebecca asks her to tell them what exactly happened as it could be very helpful. Emerson tells her that the kidnapper knows what happened to her. She tells them that she was fourteen and Sonny had asked her to help him in a kidnapping. He started talking to her as if they were partners.
She was with him for 3 months; after which she escaped and informed the police. Rebecca asked her, where she was kept but it looks like she was living with him; as she wasn’t tortured, or handcuffed. Rebecca feels that she knows more; but Emerson tells her that they cannot press her because they could lose her and that will make finding Sonny more difficult. He tells Rebecca that he will summon her when the time comes. She leaves. Rebecca is in her apartment when Ray visits her. He tells her that Emerson has got people watching him and is infuriated about it. Even Rebecca feels that Ray knows where Tommy is. Ray denies knowing about Tommy’s whereabouts. Ray tells her that he “is” a bad guy and Rebecca’s doubts are affirmed. Back in Alcatraz, Hicks is annoyed and tells Sonny that his men, who went searching for the cash Sonny was talking about, found nothing. Sonny doesn’t believe this and tells him that they might have gone to the wrong address. Hicks tells him that the box was there but there was no money in it and then stabs Sonny.
Back in the present, David tells Sonny to call his wife and take all the money he needed. Back again in the prison, the doctor tells him that he died and came back to life; no pulse for 30 seconds! Warden Edwin tells him that it was his third day in prison and he got stabbed; and that was a record. In the present, Sonny Burnett calls for ransom. The team traces the call and the address appears to be the same location, where David’s wife was kidnapped and kept and a hundred thousand dollars is the same amount he asked for on his last job; when he got caught. The team goes to the placed told by Sonny. It’s Berkley Downs, a racecourse. They check the place and lay a trap. At the Pierce residence, a cop sitting outside in the police car is shot. It’s Sonny and David’s wife is stupefied on seeing him. She could not believe her eyes as she was told that Sonny was dead. Sonny tells her that she had betrayed him.
He tells her that she said that she loved him and despite that had set him up. He had loved her. But he also had lost everything in life; and now she (Helen) would know it too. He tells her that David is in the stable, where he has sent the cops. David is dead. Rebecca knows that it’s not about the money. Emerson tells her that Sonny was in the house with Helen, to tell her that he killed her husband; and also he killed two cops who were watching her. Rebecca infers that he wants to torment her and that was the only reason he killed David in a gruesome manner. She tells Emerson that Helen’s family should be protected. Sonny could harm anyone she cared for. Soto and Rebecca feel that there is something Helen is hiding from them. Nicky is disturbed by the way David was killed and says that Sonny needs to be killed. But Emerson wants all of them alive. At the house, Helen tells the team that Sonny had aged a day. He was exactly the way she last saw him.
Emerson tries to skirt away from that topic saying that there is no rational explanation for that. Helen tells them that he had told her about the place where he hid the money from his last job; and after he went to jail, she went there and took that money. While Doc and Rebecca find an address from matching tire tracks, Sonny flashes back to days in Alcatraz of vicious physical training, which he uses to assault one of Hicks’ men in the yard, and hopefully improve his reputation. Rebecca infiltrates Sonny’s hideout and finds the full body of Mr. Pierce, the saw he used, as well as information on Helen’s daughter’s incoming flight. When the young girl arrives at the airport, Sonny poses as a limo driver to pick her up. He next creepily picks up some supplies at a local hardware store, before flashing back to Deputy Warden Tiller bringing him a hearty meal for his training, and reminding him that his little show of beating up Vicks’ crony won’t be enough to protect himself.
A little creative detective work and investigation leads the Alcatraz team to realize that Sonny intends to bury Helen’s daughter alive, likely in the same location he left the money. They manage to track down Sonny’s stolen towncar via GPS, and a high-speed chase away from the buried girl erupts, while Sonny flashes back to having violently attacked Hicks in the Alcatraz yard, even gouging the man’s eyes out. Warden James observes that Sonny has undergone quite a transformation, but reminds Deputy Warden Tiller to remember his own place in the pecking order as a member of James’ wolf pack. Back in the present the police manage to stop Sonny’s car and take the man alive, and the combined efforts of police and firemen successfully recover the girl from her burial.
Later, Rebecca assures Helen that Sonny will be out of her life forever, before musing with Doc that they too will have to answer for the things they’ve done in the Alcatraz investigations one day. In New Alcatraz, Dr. Beauregard informs Hauser that Sonny’s blood lacks the colloidal silver to cure Lucy, as not every prisoner was “taken an interest in.” Hauser angrily swallows defeat as across town, Tommy Madsen once more observes his granddaughter sleeping.