Michael Scofield and the team race against time trying to devise a plan to steal Scylla, as the Company will move Scylla to an unknown location on that same day. Michael, however, continues to suffer from his deteriorating health, and the team is forced to carry out the plan as Michael reluctantly agrees to have surgery that day. To reach Scylla, they must break through a concrete wall and a glass wall, without making any noise, changing the room temperature, or touching the floor.
Meanwhile, Gretchen dresses up to seduce the General and steal the sixth card that is necessary to decode Scylla. Having personally trained her, the General realizes that she is lying and threatens to kill her. Gretchen pleads with him, mentioning her daughter, whose father is supposedly the General. The General lets Gretchen go but tells her if he ever sees her again, he'd kill her.
T-Bag suddenly shows reluctance in continuing with the Scylla heist, as he now has a respectable job and a comfortable life as Cole Pfeiffer. However, he forces himself to refuse a complementary cruise trip offered by his boss, as it leaves that same day. Mr. Feng barges into GATE again and demands Scylla, but Gretchen again promises to deliver and asks for his help.
Even though Gretchen failed to steal the sixth card, Michael and his team proceed to steal Scylla. Michael, from a sense of guilt of leaving others in peril, changes his mind and joins the team after getting some injections from Sara. Via the underground tunnels from GATE to the Company headquarters, Michael, Lincoln, Sucre, and Mahone reach the concrete wall. They manage to break through with slow drilling, some umbrellas to catch the falling debris inside, and electromagnets to disrupt the steel linings inside the wall so that it can be dug silently.
Trishanne, T-Bag's assistant, listens to a call between T-Bag and Gretchen and alerts Agent Self. Self and Trishanne raid the address mentioned in the call, but end up in the hands of Mr. Feng after they are set up by Gretchen and T-Bag. Gretchen and T-Bag prepare to take Scylla for themselves once Michael and his team successfully retrieve it.
In silence, Sucre assembles a ladder above the floor, one rung at a time, to traverse the alarm-rigged floor and reach the glass wall. To fool the temperature sensor, he releases liquid nitrogen inside the room. Sucre loses balance when the ladder shakes, but manages to grab the falling liquid nitrogen container and makes it back up. After several tense moments, Sucre completes the ladder to the glass wall. Although suffering from occasional pain, Michael crosses the ladder and makes a hole in the glass. As he approaches Scylla and goes to take it, a sensor goes off and alerts the General. Krantz calls for security and comes after Scylla himself.
- Sucre recalls the time he was drilling through a wall with an egg-beater as part of Michael's plan to escape Fox River, which they started during in the episode "Riots, Drills and the Devil, Part 1".
- "The silent break-in stands out as a clever and gripping means to make a dramatic episode."
- ―The TV Critic's Review