The angry team demands that Agent Self deliver Bellick's body to his mother. Gretchen hands over the missing pages from the Bird Book and tells them the Company is planning to move Scylla. Meanwhile, Lisa informs Pad Man that they've hit a snag with Scylla but that it will be gone by morning.
Michael assembles the pages like a jigsaw puzzle into a map. It reveals the name "David Baker." Sara researches that there is a man with that name involved in city planning. Suddenly, Michael faints. Sara drives him to the hospital and gets him admitted to the E.R. under an assumed name. He undergoes a CAT scan.
Trishanne gives T-Bag the background check on Gretchen. She slips up and mentions the name Whistler. This alarms T-Bag, and he questions the Gate boss about Trishanne. She only started as a temp right before he arrived. Gretchen comes to see T-Bag to tell him about Scylla moving. She says that when Michael grabs Scylla, they should take it from him. Lincoln and Sucre show up at the office.
Scuderi questions Pad Man about Scylla moving. Pad Man has David Baker summoned to speed things up. Meanwhile, Mahone goes to Baker's residence pretending to be from The Company. Baker tells him that Scylla would create a new society, but then realizes that Mahone is lying. Mahone pleads for his help but members of The Company arrive at the house.
Underneath the Gate in the tunnels, Sucre tells Lincoln that Bellick saved his life in Sona. They climb through the sleeve pipe to the other side and hit a wall. Sucre steps on an explosive mine and cannot lift his foot without it being blown off. They question whether Gretchen set them up, so Lincoln goes back above ground to forcibly get her. She thinks the booby-trap looks like an anti-personnel landmine used in war and offers to defuse it.
At the hospital, the doctor knows who Michael is but still wants to help. Seeing the police show up, Michael and Sara flee.
Trishanne admits to Self that she screwed up, but that she is committed to bringing down the Company. She is a cop.
Lincoln calls Mahone about the mine. Mahone spots the Company guys and runs out of Baker's house. Baker is captured. Baker's wife finds Mahone on the hillside and gives him the legend to the map for Scylla. Mahone brings it back to the warehouse and Michael realizes that the mines under Sucre's foot aren't really mines -- they are an alarm. Yet there is a manual override.
As Gretchen starts to dismantle the mine under Sucre's foot, Mahone shows up at the Gate office. He hurries underground and tells Gretchen to stop. Mahone turns off the manual override but Sucre is afraid to take his foot off. He does, and the buzzing shuts off. He is saved.
Back at the warehouse, Michael tells Lincoln about what happened at the hospital. Self brings Bellick's body for the team to say goodbye. Sucre calls Mrs. Bellick to give her the news.
T-Bag gets Trishanne's job application and calls her reference. Self answers the phone.
While Michael works on a new plan to access the fortified wall blocking Scylla underground, Sara gets a call from the hospital. Michael's tumor has grown and he needs surgery tomorrow. Any later and he could die.