In Assassin's Creed Rogue, Shay Cormac is the Templar protagonist who was formerly an Assassin.
Shay Patrick Cormac begins the game as an Assassin operating in the North Atlantic during the Seven Years' War. After a catastrophic mission connected to an earthquake in Lisbon, he loses faith in the Brotherhood's methods and eventually joins the Templars.
The game reverses the usual viewpoint by presenting the conflict largely through Shay's Templar allegiance. He hunts former allies and encounters figures linked to Assassin's Creed III and Assassin's Creed Unity, connecting Rogue's story to both games.
Haytham Kenway is also a Templar protagonist in Assassin's Creed III, but he does not begin as an Assassin in that game. Charles Lee and Liam O'Brien are important characters, not the central playable figure.