When Oliver Queen is arrested for his crimes as the Green Arrow and sentenced to death, Barry Allen devises a plan to help his friend, who has always been like a brother to him. With the assistance of the former criminal Leonard Snart, Barry studies the blueprints of Slabside Prison, a supermax facility for high-risk offenders. Together, Barry and Leonard develop a plan to tattoo the blueprints on Barry's body, disguising them as religious designs. Barry then takes Leonard back to the past where he originally found him, before returning to the present. Barry then robs a bank to get himself thrown into Slabside Prison.

After Barry Allen and his team, the Breakout Syndicate, escape from Slabside Maximum Security Prison, they encounter a foe as clever as Barry: Special Agent Alexander Mahone. While trying to flee the United States, they face challenges along the way. Will they make it to Panama?

Barry Allen was arrested for the murder of William Kim to protect Sara Tancredi from arrest. He was placed in Sona Federal Penitentiary, under the name Michael Scofield, where he must learn to survive, as there are no guards inside the prison, only outside. Barry Allen discovers that the Company wanted him in Sona to get one of their men out, James Whistler. Will he make it out?