The show begins with the gang clearly still upset following Bellick's death. Though he initially wanted to leave him a John Doe, Self agrees to send Bellick's body to his mother. Self and Michael meet Gretchen and get the rest of the bird book pages. During the meeting she tells them The Company is planning to move Scylla.
A quick cut to a Company meeting tells us Scylla is being packed-up and will be moved by the following morning. The General suggest they contact David Baker, but he's told it will not be necessary, that the operation can be handled "in-house."
Michael and Self put the rest of the pages together to get a full view of the Company's basement. Michael and Mahone figure out a hidden message on the map with David Baker's name and determine they must see him to fully understand the blueprints.
T-Bag's secretary Trishanne brings him a file on Gretchen. While they discuss Gretchen, Trishanne mentions the name Whistler which seems to greatly interest T-Bag.
After finding a location for David Baker, Lincoln and Sucre are sent down the basement, despite the group not having completely figured out what is down there in terms of security. Michael has another one of his 'episodes,' and Sara takes him to the hospital.
After asking his boss for background on Trishanne, T-Bag is asked if he will speak at an upcoming meeting. Gretchen comes into the office and tells T-Bag that Scylla is being moved. Gretchen tells them the plan will remain the same, so that Michael and his cohorts will assume the risk in the event Scylla is gone before they get there. Lincoln and Sucre arrive to begin work down in the basement, informing T-Bag that Bellick has been killed. Sara and Michael get to the hospital, where Sarah hears for the first time that there is a history of neurological problems in Michael's family.
When it looks like there are problems moving Scylla which may delay the process, the General picks up the phone and asks the voice to "get David Baker." We next cut to Mahone, who shows up at Baker's house pretending to be working logistics for The Company. While down in the basement Lincoln and Sucre come upon the wall leading to Scylla. Sucre steps on a circle in the floor which Lincoln tells him is a mine and that if Sucre moves he will die.
Just before having a CAT Scan, Michael admits to Sara that he's not sure he wants to know what might be wrong with him. Mahone and Baker talk further in Baker's study. When Mahone said The Company had been having trouble with Scylla, Baker asks, "Didn't you read the legend?" Baker seems to figure out Mahone isn't telling the truth.
After Sucre wonders whether Gretchen might have set them up, Lincoln walks up to T-Bag's office and brings her down to where they were working. Using an emotional story about Bellick, T-Bag performs well in his meeting.
Mahone and Baker engage in a philosophical discussion about The Company, with Mahone trying to convince Baker to help him just as current Company agents arrive at the door. Gretchen recognizes the mine Sucre is standing on, telling him that the only way to disable the device is for him to slide his foot to allow her access to the firing pin. While waiting for test results Michael and Sara see police and decide to leave and have the doctor call them with the results.
We see Trishanne walk into Self's office and we learn from their conversation that she is an FBI agent working undercover. Despite her Whistler-related verbal slip-up and being fearful of T-Bag she elects to stay with the mission, telling Self "I think we can bring The Company down."
Without getting any help from Baker, Mahone gets away from the Company agents at his house. Mahone makes it down a hill to his car on the street below. Just then Baker's wife pulls up, telling him the best route to take and handing him a copy of the Scylla legend.
With Gretchen trying to convince a fearful Sucre to slide his foot an inch so she can disable the mine, Mahone and Michael use the legend to determine that any manual attempt to deactivate the mines will result in Scylla alarms being activated. Nobody is answering their phones down in the basement, but Mahone manages to get there just before Gretchen disabled the explosive. Mahone disconnects the power through a nearby panel and Sucre (after whimpering like a little girl) steps off the mine safely.
Self brings Bellick's body to the warehouse on its way to his mother and the group has a brief, impromptu ceremony. Bellick had tried unsuccessfully to become a cop, and before the casket is closed Mahone places the cop badge that Bellick held back from the 'Eagles and Angels' episode on Bellick's chest.
T-Bag's boss gives him Trishanne's file. T-Bag dials one of the contact numbers, hanging up after hearing Self's voice on the other line. Now with the aid of a legend, Michael breaks down the security devices around Scylla. Basically it will be just about impossible to get to Scylla, but Michael is "working on something."
In the meantime Sara has gotten a call from the hospital with Michael's test result. She tells him he has a rare condition related to his Hypothalamus that is getting worse and requires surgery. Michael says he wants two more days, but Sara tells him the doctors say he needs surgery the following day or he could die "and there is no alternative."