FBI Special Agent Alexander Mahone was assigned to investigate and track the Fox River Penitentiary escapees. He meticulously reviewed the files of each fugitive. Upon hearing that Michael Scofield was the mastermind, Mahone paid particular attention to his records. At a press conference, Mahone cited past cases and called upon the entire nation to be on the lookout for the eight wanted fugitives.
A furious Bellick, leading a team of prison guards and bloodhounds, chased Michael and the others to a railway line. Using a passing train as cover, Michael's group temporarily evaded Bellick. After catching their breath, the men began complaining about Abruzzi's plane failing to appear. "Tweener" mentioned Westmoreland's $5 million, but Michael quickly cut him off.
Mahone questioned Warden Pope about Sara Tancredi's role in the escape. Pope told him, "She can't answer any questions right now." Sara, having overdosed, was in a deep coma, on a ventilator, her fate hanging in the balance. However, in the deepest recesses of her consciousness, memories of her time with Michael flashed rapidly. Suddenly, Sara woke up with a sharp gasp.
The injured "T-Bag" discovered a cooler full of ice at a campsite, which he used to preserve his severed hand before staggering on. Mahone decided to investigate Michael's tattoos for clues, an approach Bellick dismissed. Veronica, trapped in the house in Montana with Terrence Steadman, tried to convince him to end his confinement and bring the whole affair to a close. Steadman told her he could only survive by remaining there.
Veronica used her phone to call the police, and Steadman didn't try hard to stop her. T-Bag arrived at a private clinic and forced Dr. Marvin Gudat, at screwdriver-point, to reattach his hand. Michael told Lincoln that Abruzzi's plane was only one part of the plan; he had a backup prepared at "Ripe Chance Woods." At FBI headquarters, after speaking with a tattoo artist, Mahone began to understand the secret plan hidden within Michael's tattoos.
Michael and the others were discovered by a father and daughter. Abruzzi threatened the young girl, allowing the group to steal their car and escape. Michael told "Tweener" their next destination was Oswego. Mahone went to Michael's old house, searching for any leftover clues to understand his mindset. Bellick, obtaining a lead from credit card records, also headed to Oswego to find a storage unit rented by Michael.
As Michael and the others were about to leave the storage unit with shovels and tools, Bellick, armed and ready, waited outside. The door was flung open, revealing an empty space. Bellick had been fooled again, leaving him furious. Meanwhile, Mahone realized that "Ripe Chance Woods" was an anagram for a person's name.
The escapees proceeded to a cemetery, where they dug up a cache of civilian clothes and money Michael had buried earlier, changing into their new disguises. Mahone arrived but they blended into a crowd, avoiding detection.
Police arrived at Steadman's residence. Veronica, who was on the phone with Lincoln, was met not with rescue, but with a bullet to the forehead. In the hospital, Sara found a paper crane in a bag brought by Nurse Katie. On it was a note left for her by Michael.