Michael insists to Mahone that he's going to find a way to save both Lincoln and Sara. Mahone persuades him to go after Linc first. Meanwhile, Christina contemptuously calls Linc "the dumb one" and is sickened that Michael cares for him so much. Michael calls and says he'll give her Scylla; just meet him at a shipping yard in 45 minutes. Elsewhere, General Krantz tells Sara that if she'd just left the infirmary door locked back at Fox River, her father and so many others would still be alive, and now none of it will have been worth it. Michael's sure to return Scylla because his heart always betrays his better judgment. Sara parries that that's true - because if Michael had used his better judgment, he's have killed Krantz the night he stole Scylla. Krantz, enraged, leaves her with T-Bag... who, leering, turns out his pocket and makes Sara fondle it.
At the shipping yard, as Michael prepares a box of homemade explosives, Mahone tries to persuade him to simply give Scylla to Christina in order to save everyone - including Pam, LJ and Sofia. Michael won't countenance any deals. Christina arrives; Linc's in the Range Rover with Downey, cuffed. She demands Scylla and walks towards Michael... but stops short of the tripwire he's set up. Michael tries to goad her into coming closer, she instead she orders her henchman to kill Michael. The henchman trips the wire and is blown to pieces. Christina gets away and holes up in an abandoned office. She tells Linc he won't live long enough to be an uncle. Linc is thrown by this, and Christina realizes that Sara still hasn't told anybody that she's pregnant.
Downey tells Chrisina that Prime Minister Banerjee is calling, wanting to know why he hasn't gotten the Scylla technology yet. Christina tells Linc that Michael's got ten minutes. Meanwhile, Krantz calls Michael. Michael says that every Fed and cop in town is looking for him, and it's impeding his return; if he's caught, Scylla will be locked away as evidence. Krantz gives him an hour, or he'll turn T-Bag loose on Sara. T-Bag gloats to Sara that when this is over, Krantz will employ him. Sara tells him there's no way that'll happen; Krantz will have him killed along with the rest of them... but if he helps her escape and get back to Michael, the slate will be wiped clean. T-Bag says that that slate will never be clean... as if he doesn't come back soon, it'll get a lot dirtier. Michael calls Christina, demanding to talk to Linc. Linc tells him that Sara's pregnant and exhorts him to go after Sara; Linc's willing to die knowing that he did something to pay Michael back. Christina grabs the phone away and hangs it up.
Self wakes up in the hospital, where a pair of FBI agents question him as to Michael and Linc's whereabouts, and begin to torture him when he won't talk; since he's impeding an investigation into an act of terrorism, he has no legal protection. Self finally says he doesn't know where they are, but he can find out. He demands immunity.
In Chicago, Sucre, still spooked by every police car he sees, is tailed by somebody. He is chased into an alleyway, turns to fight, and realizes who his pursuer is... it's C-Note. The two talk in a diner. They're both home and happy with their children. C-Note claims that he was looking for Sucre because the case against Mahone fell apart, so the Feds reneged on his deal and were gonna send him back to Fox River. He needs to know how to get a hold of Michael and Linc. Sucre is suspicious of his motives and nearly leaves, but C-Note insists that he's trying to help. The brothers are in trouble, and will only get out of it if Sucre helps him find them. Sucre doesn't want to risk losing his family again, but C-Note says that with the menial jobs he has to work because he's afraid of being arrested, he's not going to be able to support his family for very long. C-Note's sure the guy who contacted him is a player. He wants to get some device into the right hands by finding Michael and Linc, and then he'll get their records clean. He takes Sucre to meet the man. We don't see his face, but we do see his hands... and he's wearing a ring, a familiar ring with an eagle on it.
As Michael checks the Scylla briefcase, Mahone asks him how they can save Pam as well, but Michael doesn't have a plan. He tells Mahone that if there's anything he needs to do to save Pam, he should just do it. Elsewhere, Christina cruelly taunts Linc, telling him he's stupid and she never cared for him because he's not really her son. She's further enraged when Banerjee leaves the country, no longer trusting that Christina will deliver Scylla. Linc's just cost her three quarters of a billion dollars. She's about to shoot Linc when Mahone calls, offering her Scylla in return for protection for his family, and Linc's release as well. He owes Linc. Meanwhile, Michael calls Krantz, who wants to make the exchange at a parking lot in twenty minutes; Scylla for Sara. As Michael hangs up, we see Mahone put down a newly-purchased duplicate of the Scylla briefcase; Michael doesn't seem to have noticed the switch, and takes the empty case. Krantz leaves with Ralph; he's planning on killing Michael. He leaves Sara behind for T-Bag to do as he pleases.
Mahone meets with Christina. He wants her to make the call to have her people protect Pam before he hands over Scylla, but she insists he hand it over first. Downey tells Pam that a mole in the FBI has reported that two agents are talking to Self, who is getting immunity. Christina thinks he's a threat. Meanwhile, Self calls Michael, but Michael won't talk, and simply says that the whole thing will be over soon before hanging up. The FBI agents are asked by a doctor to leave the room... but it's not a doctor. It's Downey, who drugs Self via his IV and holds him down as he begins to twitch.
Michael leaves the Scylla briefcase at the parking lot. Krantz and Ralph arrive and find that the briefcase is empty. Michael seems to be hiding, and he uncoils a rope. Back at the loft, T-Bag prepares to rape Sara. Sara realizes that one of the bars she's cuffed to is loose, and to buy time, begins taunting T-Bag, telling him that his medical records at Fox River indicate that he's impotent. Just as an enraged T-Bag is finally about to attack, she gets a bar free and swings it at him, but T-Bag quickly overpowers her. Just as he begins to unzip his pants, he's smashed over the head by Michael, who we find wasn't at the parking lot when Krantz got there; he was scaling the loft to enter through he window. Michael's about to smash T-Bag's skull in with the bar, but Sara's terrified cries bring him back to his senses. The two embrace.
Christina takes Scylla from the briefcase Mahone gave her. Mahone again asks her to make the call to protect Pam, but she says she needs to make sure it works first and locks him in the side room with Linc. He tells Linc that he's there to save him. Meanwhile, we see that Michael also seems to have Scylla. In flashback, we again see Michael tell Mahone that if there's anything he needs to do to save Pam, he should just do it. And then we see what happened directly afterwards: Michael finally came up with a plan. Christina prides herself on being able to read Michael's every move... but she won't be able to predict Mahone's actions. He removes Scylla's guts and replaces them with explosives. Michael's still got Scylla's interior. He knew Krantz would never honor the arrangement. Both Scyllas, the ones given to Krantz and to Christina, are actually bombs. Back in the present moment, as Sara and Michael plan to start their lives anew, Mahone drags a weak and groggy Linc to the far side of the side room and asks if he's ready to get out of there. In the next room, Downey finds he isn't getting a connection to Scylla. Christina realizes that Michael has tricked her. And we see the red blinking light of the bomb inside the Scylla case.