The Company sends photos to Lincoln, Mahone, T-Bag and Self of people they care about - a threat. General Krantz calls; this is his work, making sure they're properly motivated to retrieve Scylla. Lincoln tells him they're looking into the keys they got from the man they shot. Krantz tells them somebody else is after Scylla - Michael. And the Company will shoot him on sight if he's found. Meanwhile, Michael and Sara, while emerging from a roadside pizza joint, are ambushed by a Company gunman. They barely manage to escape. Back in Miami, Mahone realizes that the keys have computer chips in them; Hold-Secure, the company that makes the keys probably has a database that will help them locate what the keys unlock. He finds that one lock is in Little Havana; T-Bag and Self are dispatched there. The other is down by the water; Mahone and Lincoln will go. Mahone's online probing is noted by Downey, who reports to Christina - Michael and Lincoln's mother - that someone just tried to access Carruth's Hold-Secure account. He also warns Christina that Michael has escaped and is likely heading to Miami. Christina wishes her sons understood what she's trying to do.
Michael and Sara don't have enough money for a car or a plane, so Michael calls Lincoln. Lincoln's upset that Michael escaped and jeopardized their deal with the General; it was their only chance to get their lives back. Michael doesn't believe that, and he'll do anything to stop Lincoln from returning Scylla to the Company... and he stuns Lincoln by telling him that their mother is alive. As a patrol car arrives, Michael and Lincoln hurriedly bribe a Dallas-bound truck driver to carry them in the back of his truck. Meanwhile, Lincoln and Mahone arrive at the Miami mansion near the water - Christina's place. There's nobody there. Lincoln finds a childhood picture of himself with a pregnant Christina. Mahone realizes that Christina probably has Scylla.
In the truck, Michael wonders how his mother could be a Company agent, and watch for years as her children were hunted down. Perhaps she was brainwashed the same way they just tried to brainwash him. Meanwhile, Krantz and cardholder Oren are in a limo in the middle of nowhere. Oren has the limo pull over behind a parked car and says goodbye. Krantz finds he's locked into the car. He struggles to free himself. Oren pushes a button on a detonator, and the limo explodes.
T-Bag and Self arrive at a ramshackle storefront church. T-Bag enters, claiming to be studying Caribbean religions, but the priest won't let him enter the sanctuary, which is where the lock is. Two hulking men bar the way, and T-Bag is ejected from the church. Meanwhile, Mahone's sure Christina left the photo for Lincoln to find; maybe there's a fingerprint on it or some other clue. Lincoln can't remember anything about the day the photo was taken. And so far as he's concerned, she's not his mother. She's just another person standing in the way of his freedom. Back in the truck, Michael muses on how, as a child, his mother seemed to know him better than he knew himself. He wonders if maybe, after twenty-three years, she somehow still does. Suddenly, the truck is pulled over by a plainclothes cop who insists on looking in the back. Michael and Sara hide, but the cop spots signs of them peeking out. He pretends he hasn't seen anything and closes up the back of the truck, then shoots the driver and steals the truck. He calls somebody and says, "I've got them." Michael tries to call Lincoln, but there's no signal. They can't get the back door open to escape, so Michael uses a spreader bar to try to shove a vending machine against the side door.
Christina calls Oren; she's found that the General is still alive; a Company medical chopper took him back to Los Angeles. She has Oren's driver shoot him for his failure. Meanwhile, Lincoln realizes that the car in the picture in a '78 Zephyr, but Michael was born in '76. The picture has been doctored. Perhaps the car's licence plate, MLK441, is a clue. Martin Luther King Blvd. intersects with Route 441 just five miles north of the mansion. As T-Bag and Self arrive, Lincoln insists he'll check out this lead himself. He's hoping his mother's no longer a Company agent. He sends the others back to the church. Meanwhile, Christina voice a hope that she's about to change the world. Downey warns her that their chances of success has dropped substantially in the last day. It's time for contingency plans. Christina insists on going forward; they only need a few more days. Suddenly, the General calls. He's sure Christina ordered him killed and wants to sit down and chat. She claims innocence and tells him not to call again until he has Scylla.
Lincoln arrives at MLK and 441 and finds a plaza with a fancy restaurant, empty of customers. Christina is there to meet him. She says Scylla is "safe" but won't say where it is. Lincoln says they have nothing to talk about, then. She says she's not a monster, and that the Company is a body that bends to the will of the head. If that head - General Krantz - were removed, and replaced with a mother, that'd be different. Lincoln shoots back that she's not a mother. A mother's top priority is her family. Christina says if Lincoln will just give her two days to deal with the General, she can give him and Michael their freedom. Lincoln agrees. However, there's no way for him to get in touch with Christina in the meantime. After she leaves, Lincoln closes his eyes, collapsing for a moment from the emotional strain he's been hiding.
As Mahone, Self and T-Bag stake out the church, Self makes Mahone promise that if Christina has Scylla and the only way to get it back is to kill her, he pulls the trigger. They enter the church, where Self claims to be part of a Homeland Security investigation of the ritual slaughter of chickens. Once again, the priest refuses to let them enter the sanctuary, but Mahone and T-Bag insist while Self leads a hulking guy outside. As they enter the sanctuary, the priest pulls a gun. Mahone and T-Bag overpower him and then unlock the secure door, where they find a cache of automatic weapons and fake IDs. Another associate of the priest gets the drop on them, and they are about to be executed when Self returns and shoots the priest and his man. The other guy ran away; they need to leave now before he returns with help.
Michael and Sara finally escape from the truck. Their abductor pulls over and gives chase, gun drawn, and corners them in a warehouse, but Michael gets the drop on him with a two by four. He takes the man's wallet and finds a scrap of paper with a mysterious code on it. The man, dying, tells him he won't win - and that he wasn't sent by Krantz.
Lincoln, Mahone, T-Bag and Self reunite. Lincoln says they're gonna lay low for a couple of days. The others are incredulous and are sure Christina is lying to him about changing the Company's non-violent ways. He's stunned when presented with the weapons and IDs. The date on the IDs is two days away. Lincoln, conflicted, insists on seeing her again; he's convinced they can talk this out. Mahone tells him that she told him not to come back; that was a warning. However, Lincoln returns to the plaza anyway. A sniper has him in his sights. In Christina's hotel room, Downey tells Christina that Lincoln's more of a threat than they imagined. He found the mansion and the stash at the church. He's not going to stop. They've got a clean shot right now to take Lincoln out. Christina agonizes for a moment... then orders Lincoln killed.