In Assassin's Creed Rogue, Shay Cormac becomes a Templar after changing sides.
Shay Patrick Cormac begins the game as an Assassin operating in the North Atlantic during the Seven Years' War. After a disastrous mission connected to an earthquake in Lisbon, he becomes disillusioned with the Brotherhood's methods and goals. He eventually turns against his former allies and joins the Templar Order.
That reversal is the central premise of Rogue. Instead of controlling an Assassin who hunts Templars, the player follows a former Assassin who pursues members of the Brotherhood. The change also affects gameplay, because Shay must defend himself against Assassin pursuers and recognizes familiar tactics from his previous life.
Haytham Kenway is another important Templar character in the wider series, but he is not the protagonist who changes allegiance in Rogue. Arno Dorian belongs to Assassin's Creed Unity, and Charles Lee is a Templar antagonist in Assassin's Creed III.