In Assassin's Creed III, the protagonist uses the Kanien'kehá:ka name Ratonhnhaké:ton.
The character is widely called Connor in the game and in most English-language discussions, but Ratonhnhaké:ton is his name within his Kanien'kehá:ka community. He is the son of the British Templar Haytham Kenway and the Kanien'kehá:ka woman Kaniehtí:io. As the story progresses, he becomes involved with the Assassin Brotherhood and the American Revolution.
The use of two names reflects the character's divided cultural and political circumstances. “Connor” is the name he adopts while working with Achilles Davenport, whereas Ratonhnhaké:ton connects him to his mother's people and village. The spelling includes special characters from the orthography used for the Kanien'kehá:ka language, which is why the name is often misspelled.
This answer is different from asking who the game's protagonist is: Connor and Ratonhnhaké:ton refer to the same character, but the question asks specifically for his Kanien'kehá:ka name.