Don and Gretchen, Michael and The Company are all after Scylla. Elsewhere, T-Bag has to make a tough decision as he holds Gretchen's family hostage.
Sara gives Michael another injection tells him he needs a doctor. The lookout Lincoln keeps watching on the outside of the warehouse; when Self throws gas bombs trying to force Michael and his group to leave the place, Lincoln surprises Self, hits him on his back and brings him into the warehouse. Self justifies that his motivation was not personal, just business, and proposes to sell Scylla and share the amount among the whole group; however Gretchen appears out of the blue and balances the situation and they leave the warehouse without a shootout. Meanwhile, Mahone meets agent Lang and tells her what has happened over the last few weeks, and asks who could be trusted in the FBI since the agency and Homeland Security are compromised with infiltrated agents from The Company. General Krantz decides to chase Gretchen using a satellite; Lisa gives her resignation letter to her father. Michael does not want to sell Scylla; Sucre hides himself in the trunk of Self's car and finds the low budget Fauntleroy Hotel where Self and Gretchen are staying. He steals the remaining gas cartridges from the car and texts Lincoln. Michael hides the missing chip of Scylla in the ceiling space of the toilet, but Self sees the location using a camera he planted in the warehouse. Self calls T-Bag and asks him to kill Rita and Emily if he does not call back in two hours with the location. When the seller Ralph Becker arrives on the front door selling Bibles, T-Bag sees his ring and knock-outs the guy, telling Rita that he is a Company agent. He interrogates the man and Rita convinces T-Bag to release Ralph and T-Bag lets Emily and Rita go. However the seller is actually an agent and T-Bag is arrested by The Company. Meanwhile Mahone has a meeting with Agent Wheeler, asking to see someone he can trust; Wheeler promising a meeting with the Attorney General if Alex can provide credible intelligence against The Company. General Krantzs team locates Gretchen and Self in the hotel, but Sucre fights against Gretchen while Michael unscrews the fire escape ladder; when Self leaves the room through the fire escape, he falls on the ground and Michael punches him in the face and recovers the complete Scylla; however, he starts bleeding though his nose and faints. Self retrieves Scylla and The Company catches Michael. Sara and Sucre see on the screen of Self's notebook the hidden camera in the warehouse. When they return to their hideout, they find that Self has found the chip. When Mahone calls Lincoln and finds that Scylla was lost, he is betrayed by Agent Lang and arrested by Wheeler. Lincoln surprisingly arrives at The Company to see Michael, and General Krantz proposes the best doctors and facility for Michael's surgery in return for him retrieving Scylla, and gives a file named Tombstone II to Lincoln. Meanwhile Self kills the intermediate Vikan and his bodyguard so he can sell Scylla directly to the buyer.
- The show opens with Sara giving Michael more of the medication to stave off the brain tumor which was supposed to kill him four episodes ago. Lincoln patrols the area near the warehouse, finding a matchbook and a car near one of the buildings.
As Sucre works on a project, Michael calls Self. After Michael tells Self he would like to meet, Self begins firing gas canisters into the warehouse. Self demands they come out with the missing piece of Scylla or he will gas them out. The second canister Self fires breaks open but doesn't release any gas. As Self prepares to fire on the warehouse again, Lincoln come up from behind and knocks him out.
Gretchen arrives on scene in support of Self and he tells Michael he is disgruntled from getting nothing out of 17 years of dedicated government service. Self tells them he has a buyer willing both to pay a nine-figure price and bring down The Company. Michael tells Self he would like to meet the buyer and Self and Gretchen leave. Michael tells Lincoln they are going to stick to the plan and wait on Mahone.
Mahone meets with Felicia, his buddy from the FBI. He tells her he can bring down The Company and asks if there is anybody in the Bureau she trusts.
In his Company war room the General is hot in pursuit of everybody, using imaging software to look for any of the Scylla-stealers in the Los Angeles area.
Gretchen's sister Rita tells T-Bag that Gretchen's daughter (Emily) does not know who her real mother is. T-Bag tells Rita of his recent past as Pfeiffer, a contributing member of society, but seems to think he will never escape his criminal roots.
Lincoln wants to sell Scylla, but Michael thinks that could potentially lead to a new Company. We see both that Sucre has hidden himself in Self's car and that the gasless canister Self shot into the warehouse is a type of remote ultrasound device which will allow him to view their activities on his laptop.
Sara tells Michael he has been building up a tolerance to the medication and Michael tells her he will stop taking it. Michael and Lincoln argue over whether Michael should participate in the upcoming mission. (Michael will.) Sara thinks Lincoln would be racked with guilt if the brother who saved his life died bringing down The Company.
Self and Gretchen prepare to set up shop at a seedy hotel, the location of which Sucre calls in to Lincoln.
Just before secretly injecting himself with more medication Michael tells Lincoln that he initially thought Lincoln had been guilty of killing Terrence Steadman. After watching the trial, however, Michael was convinced of Lincoln's innocence and tells his brother he has no regrets over what has taken place. Michael re-hides the Scylla chip, an action which Self catches on his computer.
Before calling Vikan to set up the deal Gretchen forces Self to let her call Emily to ensure she's alive. Self gets T-Bag on the phone and tells him that if he doesn't hear from Self in two hours with a location for the Scylla exchange T-Bag is to kill both daughter and sister.
At this point a rather persistent Bible salesman comes to Emily's door. T-Bag attempts to shoo the man away but upon noticing a sizeable ring on his finger knocks the man out with his gun.
Felicia meets Mahone at a restarurant, bringing with her an agent who has the ear of the Attorney General. The agent tells Mahone that, despite his background, if he can provide concrete evidence against The Company he will help Mahone bring it to authorities.
Michael, Lincoln, Sara, and Sucre arrive at the hotel, with Sucre revealing to Michael that he has stolen the rest of the gas canisters Self had been firing at them.
The General's daughter quits, to which he replies "I wanted a son." The General is then told The Company has found Self and Gretchen and quickly dispatch a team to the hotel.
T-Bag continues to beat on the Bible salesman, as convinced he is working for The Company as Rita seems to be that he telling the truth. The salesman, Ralph Becker, does a convincing job protesting his innocence, tearfully telling T-Bag that the military school ring he is wearing belonged to a brother who died in Iraq.
Sucre and Sara bribe their way to Self's room and pass along the info to Michael who sends Lincoln and the gas to a roof across the street.
Self and Vikan have a contentious conversation about the buyer being on his way to get Scylla. Sucre again bribes the desk to help get Gretchen out of the room, where she promptly has a huge fist fight with Sucre. Michael sabotages the fire escape just prior to Lincoln firing gas into the room. With Sucre getting his butt handed to him, Sara sneaks up from behind and shoves Gretchen down a flight of stairs. Self tries to flee the gas with Scylla, but the fire escape drops suddenly to the ground and knocks him to his back. Michael arrives to punch Self in the face and grab Scylla, while Gretchen shoots her way out of the hotel. At this point henchmen from The Company arrive, exchanging gunfire with Gretchen who somewhere manages to get in one of their SUVs and take off.
As Michael leaves the scene with Scylla, blood starts to pour from his nostrils (Worst. Tumor. Ever.) and he falls to his back. Self grabs Scylla but is prevented from killing Michael by a shot from a Company goon. Gretchen arrives with perfect timing to whisk Self from danger and Lincoln shows up with horrible timing to watch Michael get thrown into a van and taken away.
Self and Gretchen go to the warehouse and find the missing chip.
Michael is restrained on a hospital bed, seemingly undergoing some sort of testing.
Lincoln, Sara and Sucre arrive at the warehouse and start to panic after realizing the chip is gone and they don't have anything with which to trade for Michael. With Scylla out of their hands Mahone is forced to cancel his deal with the agent.
We see that Michael is being given medical tests, and that the General is standing watch over the process.
Self and Gretchen arrive for their meeting with Vikan. T-Bag calls Self about his Becker dilemma and is told by Self to kill the man.
With Rita urging him to act the way the salesman would, T-Bag eventually decides not to go through with killing Becker. T-Bag allows Rita and Emily to leave, even giving them cash on their way out. His next act of proving he is no longer a criminal is to cut Becker's restraints. As regular viewers of the show can probably guess, Becker promptly leaps to his feet, chokes out T-Bag and calls into a superior telling someone "I've got one . . . It's Bagwell. I'm bringing him in."
The Company's doctor tells the General that only once (Hmmm.) has he seen a malignant tumor as advanced as what he sees on Michael's CAT scan. At this point Lincoln has arrived unaccompanied, asking to see his brother.
Vikan arrives to meet with Self and Gretchen. He tells Self the buyer is on his way with the money, and almost instantly after Vikan's suitcase computer proves Scylla is now fully intact Self shoots both Vikan and his driver, telling Gretchen it is to avoid having to pay Vikan his cut of the deal.
Becker leads T-Bag out of the house, on the way leaving a serious shot print on one of T-Bag's 'Cole Pfeiffer: Sales Director' business cards.
Felicia comes back inside the restaurant and tells Mahone the agent has found out the Attorney General would still like to meet with him and they will drive him to the airport for a flight to Washington. Once Mahone gets into the back seat he notices that Felicia is crying. "There is no meeting with the Attorney General, is there?" Mahone asks, before sincerely thanking Felica for everything she's done as the car drives off.
The General tells Lincoln that The Company's advanced medical team will provide Michael's surgery if Lincoln returns Scylla. Admitting that it may be tough for Lincoln to work for him, the General hands him a black folder labeled TOMSTONE II for "added incentive."