Lincoln beats up Wyatt, demanding that he tell the General that they are dead. Wyatt doesn't give in. Michael and Sara convince Lincoln that this won't work. Agent Self brings a briefcase to the warehouse, and Sara warns Wyatt that he can save himself from what might be in the briefcase if he does what they ask. Self and the guys go over the blueprints but Gretchen has the remaining Bird Book pages to complete the document.
Pad Man wants Scylla moved now and Lisa Tabak tells him that it cannot be done. He orders media saturation on Michael and the group.
T-Bag leads Michael, Lincoln, Sucre and Bellick to the trap door at The Gate offices. T-Bag's boss says that his associate is missing. T-Bag calls Gretchen, who confirms that she hid the body. A detective comes to question T-Bag about the missing guy.
When Wyatt's cell phone keeps ringing with calls from Pad Man's people, he tries convincing Sara to come up with a solution to benefit everyone. He offers to help her and Michael escape.
Mahone is furious at Wyatt, and Self must hold him back. Self promises that Mahone will eventually get his shot at Wyatt.
Michael, Lincoln, Sucre and Bellick come upon the main conduit pipe for the L.A. water supply. They start to dig under it. When this doesn't work, Michael suggests they go through the pipe. As Michael and Sucre remove the sleeve of the pipe, Lincoln and Bellick exit into T-Bag's office where he is trying to distract the detective from the banging noise below.
Agent Self's briefcase is an audio record device, where he creates an edited loop of Wyatt saying "They are all dead. It's over." He and Sara leave Mahone with Wyatt, who vows that Wyatt will suffer like his son did. Self takes Wyatt's cell phone and plays the tape to Pad Man, who is satisfied. Gretchen comes to Pad Man's office holding a gun. He explains to her that he needed to know what she knew about Whistler's plans for Scylla. Gretchen softens when Pad Man kisses her. He repeatedly calls her, "my girl."
Lincoln and Bellick go to the water station to cut off the main conduit water. Back underground, Michael and Sucre hear the water stop flowing. Michael has a sharp head pain and falls to the ground. When he recovers, he asks Sucre to cover for him.
Mahone takes the heart monitor from the ambulance they stole and attaches it to Wyatt. He tortures him by allowing the monitor to shock him back every time he passes out. Mahone forces Wyatt to apologize to Pam over the phone.
T-Bag asks Trishanne to access Gate records. He shows his boss the records to prove that the missing co-worker lied about his accounts. This was really T-Bag's misdeeds. T-Bag suggests he get the detective off the case.
Sucre cuts open the water pipe to make a hole on the opposite side of the same size. His torch stops working and Michael must help him pound the hole out by hand. Lincoln and Bellick return and have to pull the second pipe from the other side through the two holes in the main pipe.
Pad Man reveals to Gretchen the plan of Scylla. Their plan to create chaos in Laos worked, and they can do the same to America. The people will turn to the leaders of finance, military and energy to fix the rest of the country. They will be able to rebuild it the way they want. He wants her at his side. Lisa reports that Scylla can be moved by the next day, and Pad Man orders it out of Los Angeles by then. Gretchen is shocked to hear him say that Michael and Lincoln are dead.
Mahone pushes a tied up Wyatt into the river.
The guys are about to get the pipe through but the beam breaks. With the water supply starting to flow, they are running out of time. Bellick jumps into the main pipe to help wedge it in even though this will trap him inside. Lincoln pleads with him but Bellick gets the pipe to fit. The wall of water drowns him.