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After finding out they have five more Scylla cards to track down, Michael Scofield confronts Donald Self about the news. Self knows nothing about the five other cards, and orders the team to track the next one by the end of the day, or they will return to prison. While Michael discusses with the group about finding the next card, Mahone disappears to make a call to Agent Felicia Lang and asks her to find information about his son's murderer. Lincoln becomes suspicious of Mahone. In Self's office, Stanton is angered that Scofield's team has to find five more cards and decides to shut down the operation.
Sara discovers an e-mail that was sent to Stuart Tuxhorn about an arrival in London. Mahone suggests that the email is actually written in code, and Scofield quickly deciphers the contents, revealing the word "Scylla", and a four o'clock meeting. Roland then traces the e-mails to a server in Anaheim. While Sucre and Bellick stake out Tuxhorn's office, the rest head to Anaheim to hack into the main server. Sara distracts an officer by claiming that she has "a job interview with human resources", sneaking his security badge from desk and passing it to Michael. Michael and Roland find the server room on the first floor and Roland proceeds to retrieve the email. Lincoln, who is observing from afar, spots the officer confronting Sara over his security badge, and calls Michael to warn him. To stall for time, Michael activates the fire alarm. When Roland successfully retrieves the email, they realize that they are trapped in the server room. As a fire safety measure, the server room is locked down and the oxygen is sucked out of the room to prevent the spread of the fire. Fortunately, Michael manages to call Lincoln, who shows up in time with a fire axe and rescues them by smashing a window.
T-Bag finds himself on one of James Whistler's furnished apartments in Los Angeles. He later opens a Gate corporation letter, which mentions him that he would be paid $75,000 a year, with a further $10,000 commencement bonus. He contacts the director of the organization, who readily agrees to meet him. Fortunately for T-Bag, the director has never met him before, and a meeting for the next day is arranged. Elsewhere in Chicago, Wyatt interrogates Bruce Bennett, who doesn't reveal anything. Wyatt injects him with a substance which seems to disorient him, trying to make him talk. Bennett maintains that he does not know their whereabouts, but eventually reveals that Sara is somewhere in Los Angeles. With this new-found information, Wyatt shoots Bennett in the back of the head.
Back in Los Angeles, Sucre and Bellick prepare to leave when Tuxhorn does not shows up for work. However, they are quickly surrounded by armed agents and Sucre manages to text Michael a warning message, asking them simply to "Run." The gang flees after Roland learns that he is being locked out of the servers. They escape in a SUV, and a car chase ensues. The chase continues on foot when their vehicles are stuck in a gridlock and Self tracks them with their GPS ankle bracelets while they are on the run. They take temporary refuge in a tunnel where the GPS signal is lost. Michael figures out the code in the emails that leads them to the 4 pm meeting at the Newport Beach power plant. They carjack a taxi and head to the power plant. However, Self tracked them down and detains everyone except for Michael who manages to slip away with some help from Sara. Michael sneaks across the plant to the meeting between Tuxhorn and the Pad Man and discovers that the meeting was between all six cardholders. Michael records the meeting on video and turns himself in to Self back at the warehouse, presenting him with the video. With the identity of the six cardholders in the video, Self decides to let the team to continue their work. Mahone receives information from Agent Lang on his son's killer. Lincoln confronts Mahone and agrees to help him find his son's killer when the Scylla mission is over.
- Jodi Lyn O'Keefe does not appear in this episode.
- This is the first episode where Jodi Lyn O'Keefe doesn't appear since her first appearance in the Season 3 premiere.
- The fire engines that respond to the alarm at the server cluster in Anaheim are branded "Los Angeles City Fire Department." Anaheim has its own fire department that most likely would've responded.