Season 1:The story of this season started when Lincoln Burrows was mistakenly accused for murdering Terrence Steadman who is the brother of the Vice president of the United States. After two months Lincoln will be executed in Fox River State Penitentiary and there is no evidence of his innocence. Michael Scofield, who is Lincoln’s brother, decided to enter the prison purposely in order to save his brother before the death sentence after two months.
At first Michael and his cell mate Sucre started to implement Michael’s plan to rescue Lincoln. Unfortunately, Michael had to let Abruzzi who is one of the prisoners to escape with them, since he is able to arrange a plane after they escape. However, things did not go as planned where other prisoners interfered with operation and forced themselves with Michael’s group. Scofield did not agree to help other prisoners, because some of them are serial killers like T-Bag, but he had no other options.
As the story goes on Michael will face a lot of obstacles such as chopping off two of Michael's toes, replacing the escaping pipes at the last moment and many other difficulties.
Season 2:
This season begins after Michael, Lincoln and the other prisoners escaped from River Fox prison. After rescuing Lincoln, “The Company” assigned the special federal agent, Alexander Mahone, to capture the eight escapees. Furthermore, they became wanted criminals and all the authorities across the country are looking for them.
The brothers decided to look for the treasure which was buried by one of the prisoners. Coincidentally, the escapers met at the treasure location which was under one of the citizens’ garages. The prisoners pretended to be workers from Electricity Company and they told the citizen that they are going to fix a problem under the garage. While they are digging to look for the treasure T-Bag was talking and manipulating to the citizen to buy some time for the prisoners. Once they found the money, T-Bag placed the money inside a bag and ran away. After that the escapees separated from each in searching for T- Bag.
Sara discovered that her father was murdered by The Company and she has no place to go. Therefore, she turned herself in to the legal authorities in order to save Micheal and his brother. Surprisingly, Killerman whose one of the company’s agents gave a testimony to exonerate Lincoln and Sara. In fact, he was able to free both of them from the fallacious accusations since he had some solid evidences. At the end, the company tried to kill Micheal, but Sara defended him and killed that agent. Hence, Micheal decided to turn himself to the Panamanian Police in order to save Sara.
Season 3
This season has completely different plot than the previous season. In this season Micheal, Mahone, T-Bag and Bellick will each other again in the “PenitenciarĂa Federal de Sona” prison. After few days, it will be clear for Micheal that everything was set up for him by “The Company” in order to rescue a former agent, James Whistler. In turn they will give back Sera and L.J, because they are now in custody.
His brother Lincoln and Sucre will try their best to aid him from the outside and keep in track with company. Lincoln tried once to save Sara and L.J but he failed, so the company decided to kill Sara for his irresponsible action.
Ultimately, Michael teamed up with the prison leader along with other prisoners such as T-Bag and Mahone to escape the prison. However, Micheal betrayed some of them where only Whistler and Mahone escaped with him. On the other side of the prison, Sucre was suspected to be involved with some troubles, so he was forced to enter the prison.
Season 4:
The fourth season starts when Micheal decided to break down the company to avenge Sara’s death, before knowing the truth that she is still alive. Michael also knew about Whistler’s plan to break down the company, but unfortunately Whistler was shot to death in the beginning of the season. Sona Prison burned down, so Sucre and the others were able to escape during the chaos.
Don Self, homeland security agent decided to form a team called “A-Team”, where the members are Michael, Lincoln, Mahone, Sucre, Bellick and Roland Glenn, a hacker whose an IT professional in programming and hacking. He made a deal with Michael’s group and told them to retrieve the most important item in the company which is “Scylla”, the company’s black book, in order to destroy “The Company”. He promised Michael and the others to give them their freedom if they managed to accomplish that task. Later on, it appeared that Sara is not dead and she had escaped from the company agent Gretchen and rejoined with Micheal again.
The team objective now is to get the six cards from different card holders in order to open Scylla’s lock. Once they were able to get their hand on Scylla, Don Self betrayed them and took Scylla without returning their freedom back, because that was his intention from the beginning. After that Self forced the former Company agent, Gretchen to team up with him to find a buyer for Scylla. However, once they found the buyer, it turned out that he was working for another organization other than the company.