He said that he has no regrets, and that now they are all, finally, 'free'. The message tells Sara and Lincoln that Michael would have died anyway, as The Company didn't actually cure him, just delayed his death for a little while longer. At the end of the final episode, Sara is given a letter and DVD from Michael, who wanted her to have it in case he didn't make it. Sara escaped, but Michael sacrificed himself to save her and his son. In an emotional goodbye, Michael tells Sara that he will always be with her in their child, and brings two wires together, opening the door and going down in a shower of sparks. It's not a perfect solution though, as the surge will electrocute and kill him. He reveals that he knew this was a possibility, and that he can open the door by creating a power surge to override the mechanism. At the end of the tunnel, however, there is a locked door, trapping them both inside. The plan involved Michael first sneaking into the prison, and then leading Sara out through underground tunnels to freedom. Once again, Michael has to come up with a plan to break someone he loves out of prison. In this series, it is Sara who ends up in prison, arrested on her wedding day for a murder she committed to save Michael.
It is only in The Final Break, a TV movie special that wrapped up the show, that Michael finally meets his (alleged) end. However, he refuses to get the surgery, as he is too busy dealing with The Company, and the conspiracy that he, Lincoln, and Sara are attempting to uncover. Michael, now at the same age that his mother was when she died, is taken to a hospital and diagnosed with hypothalamic hamartoma a brain tumor requiring immediate surgery.
He mentioned Michael's teen years, and their mother's health issues, revealing that their mother had had similar problems before dying at 31 from an aneurysm.
At first, Michael hid his deteriorating health from his brother and Sara, but eventually, they found out, and Lincoln was appalled. He started to get nosebleeds and severe headaches, even passing out from the pain. In season 4, however, it was discovered that Michael was dying. Michael Scofield spent the first three seasons of Prison Break in seemingly perfect health - his perfect health was even an issue in season 1, when he had to trick Sara into believing that he was diabetic to gain regular access to the infirmary.