Lincoln Burrows is accused of the murder of Terrence Steadman, who is the brother of the female Vice President of the United States. With strong evidence supporting the charges of first degree murder and aggravated discharge of a firearm against him, Lincoln was sentenced to death (by electric chair). Although Lincoln adamantly asserted his innocence and that he was set up, he was sentenced to the Fox River prison facility to await his execution.

Lincoln's brother, Michael Scofield, convinced that Lincoln could not have committed such a crime, hatches an escape plan. He designed a full-body tattoo that secretly encodes every last detail of the prison facility and had it tattooed on his body. After destroying any evidence that could reveal the tattoo at his office, Michael staged a bank robbery, knowing that he will be convicted and sent to Fox River. Once an inmate, time worked against him as he overcame various obstacles and made the right connections among the inmates and prison staff to be successful in breaking out his brother.

As Michael put his plan to action inside the prison to save his brother, their childhood friend and lawyer, Veronica Donovan worked on the outside to uncover the conspiracy that put Lincoln in jail. She began to unravel a trail of mysterious incidences that resulted in her being pursued by covert agents. On the same night as Michael and Lincoln's successful escape from Fox River, Veronica found the strongest piece of evidence to disprove Lincoln's murder charge.......