- Chapter 6
Later Paxton is summoned by Geary during yard time pretexting that Abruzzi want to talk to him.He's conduct in the Boiler room where Abruzzi and a plenty of his men are waiting for him. Abruzzi explains that he had checked Paxton's phone reports and had discovered that he was an agent:years ago a cop under Abruzzi's payroll had betrayed him the cop name was Jack Mannix, the superior of Tom. Paxton try to claim his innocence but is beaten up by Bobbo and another of Abruzzi's goon Paxton managed to fight them off by jumping over a ledge, unfortunately his PI card had fell under a grade. He then fought his way through Aburzzi's henchmen.
In the same time two Department of Corrections's special agent: Agent Richardson and Agent Bates came to Fox River pretexting a sanitary inspection to Bellick, in fact they are two Company operatives sent to questionning Paxton about his mission: the two managed to find him and asked him why he haven't killed Burrows yet, Paxton claims that it's not his mission Richardson revealed to Paxton that Jack Mannix had sent Turk to help him and threaten him to finish his mission otherwise he will dye! Paxton then understand that his assignement was a set up that Manniw had created for him.He sneak back to the Block A and witnessed Abruzzi, the throat cut, being evacuated from the Penitentiary.
Paxton is expressing his willing to confront Mannix after having ending his mission and "terminated" Burrows, but he has a visitor from the FBI, the mysterious agent he's in fact, Aldo Burrows Company's traitor and Paxton's longtime friend and patern figure. Aldo wants help from Paxton in order to save his sons (Lincoln Burrows and Michael Scofield) from the Company's wraith, Tom denies claiming that doing anything else than killing Lincoln will result in his death. Aldo ultimately revealed him that the Company has already signed his death warrant because he haven't killed Linc yet: he's now expendable and Mannix will come soon to kill Burrows. Aldo and Tom made a deal: if Tom agree to fight against the Company Aldo will erase all the files concerning him in the outside (Army files, Company records) he will not exist. But in the time he managed to get the blueprint of the penitentiary in order to having an idea of the escape plan. Paxton is now a rogue operative of the Company determined to save the brothers and help Aldo in his fight against The Company.