In order to get a copy of the Scylla card, the gang must break into the well-guarded home of Company man Tuxhorn; and T-Bag goes to extremes to survive.

As they arrive in LA, Don insists that everybody except for Sara — the only one of the group who isn't a convicted felon — wear GPS ankle monitors as insurance against their trying to escape. The public story is that all the men have been transferred to a Supermax facility. Don introduces them to the final member of the gang, Roland Glenn, an arrogant computer genius specializing in identity theft. He rubs everyone the wrong way right from the get-go. Mahone has an idea of where to start looking for the Scylla data card. When he was waiting in the car for Whistler and Gretchen, he noticed that the Cardholder's limo driver stood in a military stance, and the limo was riding lower: weighted down by private security. The driver's suit was fancy: he's full-time, and highly paid. Find that driver, and you've found the Cardholder.

Having traced the driver, the gang scopes out Tuxhorn's home. It's practically a fortress, dripping with all kinds of security. Linc wonders if maybe Tuxhorn keeps the card on him; then they wouldn't have to break in. Roland says they don't need to get the card, just copy it. He's invented a wireless hard drive that can suck up any electronic data within ten feet of it. He used it to steal people's credit cards and PIN numbers, but it'll work on anything... so long as they can get close enough. Sucre, the device in his pocket, gets in a deliberate fender bender with Tuxhorn; but no luck: Tuxhorn doesn't have the card on him. They'll have to break into his home after all. Mahone wants to know what Sara's doing here. She claims she's just helping Michael, but she looks haunted. She's hiding something. Mahone says he knows how being held captive can make you feel. He declines to answer when Sara turns the tables, and asks what's motivating him.

T-Bag and Sancho stagger through the desert, so hungry they're reduced to eating the pulp from Whistler's bird book; though they preserve a bit that says "Gate," and another that says, "San Diego. PC line. B12. 36-24-36." Driven by desperate hunger, Sancho suddenly attacks T-Bag with a plank of wood, intending to kill and eat him. T-Bag knocks him down… and Sancho is killed, his head split on a rock. T-Bag, regretful but just as desperate, builds a bonfire and drags Sancho's body over to the flames. Wyatt takes a woman hostage in her own apartment. Her roommate, Claudia, works with the Department of Corrections. When she comes home and sees her roommate's plight, Wyatt tells her to use her high-security clearance to get him the records of prisoner transfers… and find out where Michael and Lincoln were sent.

Sara is reading a quotation from Homer's Odyssey written down by Michael and Linc's father, that they found in his files: "There is no fighting her, no power can fight her, all that avails is flight." The quote, she realizes, is from a chapter where Odysseus must confront a monster called Scylla. To pass Scylla required Odysseus to sacrifice six of his men; the only other option was to abandon his quest. Odysseus chose the sacrifice. Michael wonders if they'll have to make the same choice to bring the Company down. Sara thinks it's worth it: maybe fate's brought them together to do this. Don goes meets with Jasper Potts, an ex-Company man now working as a used-car salesman. Jasper's not pleased to see him, and tells him to go away; he'll get them both killed. Don demands to know where the decoder box for Scylla is.

The gang has a new plan: Sara chats with Tuxhorn's housekeeper as she waits for the bus, and secretly slips the device into the housekeeper's purse. When she arrives at Tuxhorn's place, Michael calls. He claims to be from the company that installed the security, asking her to check the contacts on all the windows in order to get her to move through the house. At the end of the day, when she leaves, Bellick pretends to be a purse snatcher, with Mahone in the part of the heroic bystander. He chases Bellick around the corner, and then the two search the purse… but the device isn't there. She found it, and left it behind, thinking something belonging to Tuxhorn had simply fallen in. It's still in the house. Michael asks for more support from Don to get into the house, but Don refuses; he can't run this operation by any higher-ups. He also says that if the device is found, it's game-over for all of them.

They try their next plan: as Michael and Mahone hide behind Tuxhorn's house, Linc and Sucre set off the alarm... of the neighbor across the street. While Tuxhorn and his men are distracted by the commotion across the way — deactivating the door alarms as a sleepy Tuxhorn staggers outside — Michael and Mahone sneak in the back. Michael finds and grabs the device. It’s time to go, but Mahone is distracted by Tuxhorn's son calling out for his Daddy. He's jolted into a reverie, remembering his own murdered son. Michael manages to shake him out of it just in time, getting out the back way just as Tuxhorn is turning the alarm back on.

Wyatt finds that Bruce Bennett posted bail for Michael and Linc, and confronts him in his home. Wyatt's been scoping out the prison where Michael and Linc were reportedly transferred. No new inmates have arrived there in the last few days. Where are they? As Bruce swears he has no idea, Wyatt takes a needle and injects it into Bruce's neck, knocking him out. He then gets a phone call, and tells the person on the other end, "I don't care what she looks like. Three tablespoons of water. One of honey. Nothing more." We cut to a dingy basement where Gretchen — beaten, bruised, and starved but still very much alive — is being held. T-Bag is finally rescued by a pair of American guys riding ATV's; they give him a ride to San Diego. Once there T-Bag finds the Pacific Coast bus line — the "PC line" — and uses the code in the book to find locker B12, combination 36-24-36. Inside he finds an envelope from a corporation called "Gate;" fake ID and other documentation with Whistler's face on it; and an apartment key and address.

Back at the dockside warehouse where Michael and the others are quartered, Sara tells Michael she needs the two of them to just start over: No guilt, no responsibility. If something happens to her, she doesn't want Michael punishing himself for the rest of his life out of guilt. Roland examines the code on the copy of Scylla, and makes a terrible discovery: they've got only a slice of the information. In Homer's Odyssey, Scylla was a six-headed monster. Scylla isn't a single data card: it's six data cards, and you need all of them to decode the information properly.

Pad Man meets with Tuxhorn. He tells him that the world is changing, but he's not going to change the way he does business: the Company will change the world instead. When there's a problem on the assembly line, you don't change the product: you change the people who make it. Then he hands Tuxhorn a piece of paper with the number 10,000 on it, talks about casualties of war and acceptable loss... and asks Tuxhorn if that number is acceptable to him. Tuxhorn blanches for just a moment, and then says yes. Pad Man smiles, and says he can issue the op-order today.

Back at the warehouse Michael is washing his face when he suddenly gets a nosebleed. Linc enters, and Michael hurriedly cleans up and hides the nosebleed from his brother.