Michael and the gang pull off the Scylla heist from deep within Company headquarters, but a terrible surprise awaits them.

As an unwitting Michael is about to be caught by Pad Man, T-Bag and Gretchen (armed with machine guns) wait to double-cross him on his expected return. Meanwhile, Don and Trishanne are still tied up as Feng plots their demise. Michael is examining Scylla: it resembles a computer hard drive; but has a port for a single Scylla card rather than having six ports, as expected. Suddenly the elevator doors open, and Michael is surrounded by Pad Man's security detail… but the security guards are ambushed by Mahone, Lincoln, and Sucre. There is a standoff, which Linc tips in the gang's favor by grabbing Pad Man, and holding a gun to his head. Pad Man orders his men to lower their weapons. Michael demands that Pad Man give him his Scylla card. This was the plan all along: trigger the alarm, and trick Pad Man into coming down while bearing his card. Michael plugs the card into the port, and five other ports reveal themselves. The five other cards are stored on Roland's old laptop, and Michael plugs the laptop into the ports with a homemade USB-to-card connector. Pad Man is shocked that they even knew there was more than one card, much less that they got copies of all of them.

Don and Trishanne pretend to have an argument in order to distract the guards from the fact that Don is wriggling himself free of his bonds. He escapes, and frees Trishanne. In the ensuing firefight Trishanne kills Feng. Don sends Trishanne to GATE while he stays to mop up. Back in the Scylla room, the Scylla box unlocks and opens. The cards were keys. Inside is a solid black object about the size of a hardcover book. This is Scylla itself; but what exactly is it? Michael leads the gang to escape via the security elevator rather than back the way they came. They take Pad Man along with them. As Pad Man is marched into his office, he seems calm, and tells the guard that everything's under control. Nevertheless, the guard (Damani) grabs his phone and reports a "major situation," putting the building into lockdown. Michael seems unconcerned, and begins to examine Scylla's workings. As Michael works, Pad Man shows Linc a photo of himself, much younger… with Linc's father. Pad Man and says there's a lot Linc doesn't know about his own parents. Linc is enraged, and Mahone has to stop him from roughing Pad Man up.

As tension grows between T-Bag and Gretchen, White enters the office wanting to meet Gretchen. He notices the half-hidden bag of machine guns on the floor, gets nervous, and leaves. He's about to call somebody when Gretchen pulls a gun on him, forcing T-Bag to cooperate with her in taking everyone at GATE hostage. T-Bag's dream of a normal life is now completely shattered. Trishanne arrives at GATE not long after to find the place locked; she uses her keys to enter, and finds gagged hostages. She sees T-Bag and Gretchen tying up more on the far side of the room. They haven't seen her yet. T-Bag wants to run, but Gretchen says it's worth $125 million to wait for ten more minutes. Trishanne reveals to White that she's a Federal agent, and begins to untie the hostages while Gretchen and T-Bag are having an argument. White panics, and runs on his own; he's seen, and shot dead by Gretchen. A gunfight erupts, and Gretchen and T-Bag manage to escape. Trishanne gives chase.

Don returns to his office, where he tells his supervisor Stanton that they're almost at the finish line. Stanton says that as soon as they have Scylla, it must be brought directly to Senator Dallow's office. Pad Man notices Michael having a stab of pain. He tries to bribe the others into letting him go; no dice. Meanwhile Lisa, at her banquet, has food spilled on her by a waiter. She goes to the bathroom to clean up… and is captured and held at gunpoint by Sara. As a SWAT team with a battering ram gathers outside Pad Man's office, Michael gets a call from Sara... and Lisa. Sara will kill Lisa if Pad Man doesn't let the gang leave with Scylla. She calls Pad Man "Dad:" Lisa's his daughter. Pad Man pales. Linc demands they be taken to whatever transport was being planned for Scylla. As they head out, Lisa attempts to convince Sara that Michael and Linc are "bad men." Sara's not buying it. The Company has destroyed lives. Lisa seems shocked to hear it.

In the GATE parking lot Gretchen wipes down her gun for prints, and throws it in the dumpster. She has T-Bag do the same. She then takes out a smaller gun, and points it at T-Bag, preparing to kill him: he's the only one who can connect her to the crime scene. Just at that moment Trishanne bears down on them in a car, giving T-Bag the opportunity to flee. A passing SUV gives Gretchen a chance to escape in the opposite direction. Trishanne turns around, and pursues and captures T-Bag, identifying herself as Special Agent Miriam Holtz.

Pad Man leads the gang to an armored truck. He tells Linc that his father's real job at the Company was killing defectors. Lisa's security detail becomes suspicious. They kick down the bathroom door and find Lisa zip-tied and gagged. She is unbound, and says that Sara just left. Outside, Sara — who bribed the waiter to spill food on Lisa — makes her escape. As the gang drives the armored car away, Lisa calls Pad Man to tell him she's all right. Relieved, he turns his attentions towards retrieving Scylla. Michael calls Don to report that he has Scylla: time to rendezvous. The truck arrives at the airport. Michael and Linc don baseball caps, and separate from Mahone and Sucre. They have been followed by Ferguson, a Company guard; he’s keeping his eye on Michael's backpack, which contains Scylla. A single phone call grounds all planes. Ferguson and his agents pursue Michael and Linc through the terminal. Michael texts Mahone with the word "Now." Mahone calls the National Guard, claiming to be an off-duty cop from Chicago who just saw something suspicious at the airport. Ferguson corners Michael and Sucre, and seizes the backpack; a moment later the National Guard arrives to lead Ferguson and his men away to a security room, where Ferguson is asked to empty his backpack. All that's in there is a book: Shakespeare's All's Well That Ends Well. Sucre had Scylla all along, and Ferguson and the Company have been successfully fooled.

At the warehouse Michael hands Scylla to Don, who says he'll live up to his end of the bargain. Vans will arrive in a half hour to take them to a field office for processing… and freedom. Suddenly Michael feels faint, and Sara has to tell Don that Michael needs to get to a hospital. Don says he'll send an ambulance with the vans. He thanks Michael: lives will be changed forever because of what he's done. Everyone relaxes, anticipating freedom at last. Don leaves with Scylla, and meets up with Trishanne, who has T-Bag captive in the back of her car. They can cut a deal with T-Bag to see if there were any other buyers for Scylla: they want as many indictments as they can get. Back at the warehouse Linc tells Mahone that they're settled – the bad blood between them is forgiven. Sara points out that it's been an hour, and no ambulance yet. Michael calls Don; no answer. Back at Trishanne's car Don says, "I'm sorry," and shoots Trishanne dead. At the warehouse Michael opens the envelope Don gave him; it's full of blank papers. They've been betrayed, and Don now has Scylla.