He never fought charybdis. He had a choice to pass by scyllia or charybdis and chose scyllia. He never had to fight them a second time
Micheal and Lincoln face off with Christina and The General in the final stand for freedom. Christina is killed by Sara while Kellerman, Sucre, and C-Note come to the rescue just before the General can kill the brothers. Scylla is then handed over to the authorities and everyone is able to live normal lives. Michael and Sara are walking on the beach where Michael's nose then begins to bleed again. In the end, everyone is shown living their lives 4 years later. Mahone has begun a relationship with Lang, as has Lincoln with Sofia. T-Bag is back in Fox River, and Kellerman has become a Congressman, General Krantz was sent to the electric chair, C-Note works for UPS, Sucre was seeing his daughter and Don Self is still in a paraplegic state in a hospital. The final scene shows Lincoln, Sucre, Mahone, Sara, and Michael Jr. (her and Michael's child) at Michaels's grave where it is revealed that he had died sometime earlier. Everyone walks away ending the series.