He tortures Wyatt and extracts a confession, eventually killing him by drowning him in the ocean with a concrete block.

Having received a full pardon from the United States government, Mahone is a completely free man. He successfully reconciled with his former FBI colleague, Felicia Lang, and the two began a romantic relationship. Free from his drug addiction, free from the threat of The Company, and vindicated by his loyalty to Michael, Mahone is presumed to be living a quiet, peaceful life away from the chaos of his past.

Ultimately, Mahone successfully escapes Sona alongside Michael, Whistler, and Luis McGrath during a heavy rainstorm. Following the escape, Mahone decides to ally himself with James Whistler, working against the Company alongside a vengeful Lincoln Burrows. Season 4: Ultimate Tragedy and Alliances

FBI agents approach Mahone, offering him his old job back if he spies on Michael and exposes the escape plan. Mahone appears to accept the deal, leading viewers to wonder if he will betray his friends. However, it is revealed to be a double-cross: Mahone feeds the FBI false information, using his knowledge of Michael's tactics to ensure Sarah's successful escape. After Michael sacrifices his life to save Sarah, Mahone delivers Michael’s final video message to Sarah and Lincoln, cementing his place as a loyal ally. Season 5 (The 2017 Revival): Where Was Mahone?

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Mahone moves past his vengeance and fully commits to helping Michael destroy The Company. He finds peace with his past actions and forms a deep bond with the team. The Final Break & Season 5

He is approached by the FBI to spy on Michael in exchange for reinstatement.

However, Michael frames Mahone by hiding a massive stash of illegal drugs on his getaway boat, the Christina . Panamanian authorities arrest Mahone, and he is thrown into the federal penitentiary known as Sona—the very same prison where Michael is eventually sent. 2. Surviving the Horrors of Sona (Season 3)

Recognizing that Michael is his only ticket out of Sona, Mahone forms an uneasy alliance with his former target. Michael relies on Mahone’s tactical intelligence and physical combat skills to help orchestrate an escape plan.