Sanctuary (1998)

"Beneath the corridors of power, men without faces deploy operatives that don't exist, on missions that never happen."

Luke Kovak is part of a covert group within the CIA that works on illegal black ops involving blackmail and assassinations. When his boss orders the murder of one of the team, Luke realizes how expendable they all are and gets out (taking proof of their activities with him). He now lives as a priest until the group start to get close to tracking him down.