Michael Scofield's Death Explained

In the revival series, season 5, set many years after the original conclusion of The Final Break, and after a very dramatic and drawn out death, we discover that Michael Scofield is very much alive. At the very start of the premiere, we hear Michael's distinctive voice saying, "I died seven years ago...", followed by a speech of freedom.

Remission
For a while, Michael got Sara to treat him, as she was a doctor. But when he collapsed while attempting to steal Scylla, The Company kidnapped him and took him to their facility. Once he was there, they explained to Lincoln and Sara that they could treat him as their medical research is far more advanced than that available to the general public. They promised to operate and save Michael, but only if Lincoln retrieved Scylla for them. It was a hard but very straightforward choice, Michael's life or Scylla...

The Company operated on Michael, using an experimental procedure that has worked in the past (for Christina Scofield) but was still largely untested. As Sara watched, Michael started to flatline, before a mysterious serum was injected into his brain, allowing him to recover.

The procedure actually helped Michael, as it allowed him to understand elements of the Scylla conspiracy that he didn't before. This was thanks to Michael's Dream, that he had during his flatline.

After Michael recovered enough to escape, he and Sara flee the company, believing that Michael is cured.

A Final Sacrifice
In The Final Break, the TV movie special which wrapped up the show, Michael finally meets him alleged end. In the movie, Sara is the one who ends up in prison, arrested on her wedding day for murdering Michael's mother, Christina, in order to save Michael. Once again, Michael has to come up with a plan to break someone he loves out of prison.

Michael's ingenious plan to break Sara out of Miami-Dade Penitentiary Women's Facility, involves him sneaking into the prison, and then leading Sara out through the underground tunnels to freedom. At the end of the tunnel, however, there is a locked door, that trapped them both inside. Michael revealed that he knew this was a possibility and that he was able to open the door by creating a power surge to override the mechanism. This was not the perfect solution though, as the surge would electrocute and kill him.

In an emotional goodbye, Michael told Sara that he will always be with her in their unborn child. He then brought two wires together, opening the door and going down in a shower of sparks.

Sara escaped, but Michael sacrificed himself to have her and his son. At the end of this TV special, Sara and Lincoln were given a letter and DVD from Michael, who wanted them to have it in case he didn't make it. The letter was a doctor's report that stated that Michael was still very sick. In the DVD, Michael explained that he would have died anyway, as The Company did not actually cure him, just delayed his death for a little while longer. He st he electrocuted himself, leaving him twice as dead, which a memorial stone in place and a touching farewell message for his wife and brother.

But, because he didn't die onscreen, it left the producers with enough of a gap that if they ever wanted to pick the series back up again, they could easily find a logical reason for Michael actually being alive.

Michael did not die, supposedly the power of the electrical surge wasn't enough to kill him, just temporarily stun or knock him out. When he is then discovered underneath the prison, the government, The Company (or both) trade his freedom for the lives of Sara and Lincoln, promising to leave them alone in return for his cooperation.