The regular seasons of Prison Break ended after season 4.  This ending was a cliff hanger, with an advertisement for the prequel.  This prequel was not shown on TV, it was sold with the DVD set (the show ended in 2008).  The prequel was essential to understanding why Michael died.  In the regular season, the show fast forwarded to his closest friends and family at his grave.  Viewers did not know how or why he was dead.

Sara, Lincoln, Michael's son, Mahone and Sucre at Michael's grave

Michael died to save his wife Sara and their unborn child.  Knowing he did not have much time to live because he had a brain tumor that could not be cured.  His way of dying was justified, and some critics say it was right because of all the lives he ruined.  He did not mean to hurt anyone, but in the process of saving his family, other people were sacrificed.