The gang needs to get through a 30,000 gallon water-main to get to Scylla; T-Bag fends off an investigation; and Mahone waits for revenge on a captured Wyatt.

Linc beats a captive and tied-up Wyatt, trying to coerce him to tell Pad Man that Wyatt found and killed them. It's not working. Even if they could torture him into talking, Michael says it wouldn't work: Pad Man would hear the fear in Wyatt's voice. They need to get Wyatt to break soon, before Mahone loses his patience and kills him outright. Self arrives with a case full of... something... to help him "have a nice conversation" with Wyatt. In Pad Man's office, Lisa tells him that it will take three days to move Scylla. That's unacceptable to him. He wants it moved now, and to a location that nobody knows about rather than to their most secure facility. Wyatt's not checking in, fueling Pad Mans' apprehension. He demands that a press release go out so that Michael and the rest will be all over the news.

Michael and the others plan to get Scylla. There's a big X on the blueprint: some sort of big, unknown impediment at the end of a walkway. Gretchen has the pages that show what's on the other side. Michael, Linc, Sucre, and Bellick go to GATE and into the trap door, while T-Bag stays in the office above. Just as they disappear below, the boss (Gregory White) returns. He wants to know why Andy Blauner resigned, and why his fiancée doesn't seem to know where he is. T-Bag calls Gretchen, who assures him that the body won't be found. She is arming herself as she prepares for a meeting.

Sara doesn't want to see anybody tortured, not even Wyatt. As Wyatt's phone rings, Sara promises that if he cooperates, Don will make sure he gets life in a decent facility rather than the death penalty. As Wyatt whispers a counter-proposal, Don has to hold back Mahone from killing Wyatt. Don tells Mahone he understands what he's feeling: Don lost a child too, due to complications with his wife's pregnancy. His wife died as well. Mahone asks him what he'd do if the doctor responsible was standing right there. Don promises that when the time comes, he won't stand in Mahone's way. Wyatt tells Sara that he was forced to do things by the Company just like Mahone; if she'll just trust him, he knows people who can help her and Michael: this can all be over. Sara smiles oddly, and says, "It is over."

Michael and the others find the walkway that leads underneath Company HQ. There's an ominous droning sound in the distance, which gets louder and louder as they approach; it turns out to be the sound of 30,000 gallons of water passing through a main conduit pipe for the LA water supply, behind a huge, curved wall. It’s time to start digging, with sledgehammers, through the cement floor. Meanwhile, at GATE, Detective Conor Mara arrives to ask "Cole" (T-Bag's alias) about Blauner. The sound of the sledgehammer can be dully heard in T-Bag's office. Det. Mara says that Blauner's letter of resignation came from a copy shop, which is odd since he had a fax machine at home. The security cameras show a woman driving Blauner's car away that day. T-Bag suggests that maybe he was cheating on his wife, but Mara thinks that's unlikely: the rest of Blauner's colleagues have painted him as a Boy Scout. As he asks T-Bag how he lost his hand, he hears a particularly loud thud; T-Bag claims it's trouble with the pipes. Mara then asks if it's true that he and Blauner didn't get along. Back underground, the gang can barely make a dent: there's granite under the concrete. This isn't going to work. They're going to have to go through the pipe. As T-Bag explains to Mara that Blauner was just defending his turf against the new guy, Linc and Bellick walk right into the room. Before they can be questioned, Bellick turns to T-Bag, and pretends that they were hired to do some shelving. T-Bag sends them along, nervous about the close escape.

Don brings the case to Wyatt; it was his laptop. Wyatt's been recorded, and Don has re-edited his words to form a recording of Wyatt saying, "They are all dead. It's over." Sara tricked Wyatt into talking enough so that they'd have material to create a message. Don tells Sara to come with him… and leave Wyatt alone with Mahone. Sara's upset, knowing what's about to happen, but goes with Don nonetheless. Mahone produces a heart monitor and a car battery, preparing to torture Wyatt, and make him suffer like his son did. Then Wyatt's going to make a phone call to Pad Man… and this phone call will be effective, because Mahone wants the General to hear the fear in Wyatt's voice.

Pad Man gets the fake call from Wyatt, and decides to call off the press release about Michael and the others; it's no longer necessary. Suddenly Gretchen arrives, gun pointed at the General. He never changed the access code on the covert entrance. Pad Man tells everyone to leave them alone together. He then smiles at her, saying that he knew she'd come home. He had to let Wyatt torture her to be sure she knew nothing about Whistler's plans for Scylla. He knew she wouldn't take it personally... because she's his girl. He lowers her gun, and kisses her. She kisses him back. Linc and Bellick go to the DWP, and find the manual override to shut off the water main. Back at the pipe, as the rushing water stops, Michael says they'll have about an hour before the city repairs it. They've got 60 minutes to do 90 minutes of work. As he starts to try to cut through the pipe with a thermal lance, his vision suddenly becomes unsteady and blurry. He loses control of his hands, and slumps to the floor in a daze. A moment later he recovers a bit, and hands Sucre the torch, telling Sucre to cover for him.

T-Bag remembers Blauner accusing him of making sales with phony Social Security numbers. Hatching a plan, he has Trishanne access GATE's records, and switches his fake sales with Blauner's records. He then reports to White that Blauner was faking sales and laundering money. If Det. Mara finds this out, White will be swimming in IRS auditors. He suggests that White tell Mara he found irregularities with Blauner's personal expenses; that'll get rid of Mara without the IRS investigating. Mahone tortures Wyatt... until Wyatt apologizes to Mahone's wife Pam, over the phone, for his murder of their son.

Sucre and a dizzy Michael climb into the pipe. There are thirty minutes left… and the thermal lance goes dead. Sucre and Michael revert to sledgehammers until they make a hole in the far end. Linc and Bellick return; five minutes left. They need to run a "sleeve" through the pipe: a sort of “habitrail” they'll be able to use to get through the pipe when the water returns. Somebody will need to go into the pipe to guide it through the far hole. Bellick and Linc go through, but the sleeve crashes down and out of reach. It gets wedged… and the roar of rushing water is heard. Linc says they need to leave, and forget about Scylla. They don't have a choice. Bellick jumps back down into the pipe, grabs the sleeve, and pushes it back up so Linc can finish threading it through. Michael yells from the other end for Bellick to get out: the sleeve will block his exit. He'll be trapped. Bellick is sacrificing himself. He manages to hoist the sleeve up high enough for Linc to pull it through just as the wall of water arrives. Bellick drowns. Linc is stunned.

Gretchen tells Pad Man that she's a free agent now. She can switch sides, but only for a good offer. Pad Man tells her how well their plans are going; he wants her by his side. Gretchen asks about Lisa. Pad Man says again that Gretchen is his girl. Gretchen accepts his offer, and Pad Man lets everyone else back into the room. Lisa is defensive and unhappy about Gretchen's continued presence. She reports that Scylla can be moved tomorrow, but there's no need since Michael and Linc are dead… which comes as a surprise to Gretchen. Pad Man says to go ahead with the plan anyway.

Mahone drags Wyatt down to the docks, hands chained to a concrete block. He throws him over the edge, and watches until the air bubbles stop. Emotionally exhausted and dead-eyed — and not looking the least bit relieved or satisfied, just heartbroken — he looks at the photo of his son for a while, and then walks away. Back at the pipe, Michael continues to work. Linc is somber, repeating: "He wouldn't climb out. He just wouldn't climb out." Sucre suggests following the pipe to see where it leads to try to find Bellick; but Linc says he's gone… he's just gone.