In the IDW Comics, Raphael, like his brothers, is one of the reincarnated sons of Hamato Yoshi, who in medieval Japan were murdered by Oroku Saki. He began his new life in the present as a young turtle in the laboratory of StockGen Research, Inc., Baxter Stockman's genetics laboratory and served as a guinea pig for an experiment to be grown to be an naturally armored super soldier. Some ninja tried to seize the Turtles and various other research results from the laboratory, including a mutagen. The intervention also led his born-again father, now a lab rat, and the Ninja Turtles to be wetted with a chemical cocktail that made them ultimately mutants.
Shortly before his mutation Raphael was, however separated from his family, by the attack of a hungry street cat. In the year after his mutation he eked out a miserable existence as a vagrant on the streets of New York City without a memory of his life before his transformation, until he was befriended by Casey Jones and soon after he found his family again. In the course of his adventures with his family he also built a close relationship with the mutant fox Alopex, especially because the two are perhaps too similar in temperament and life situation.
It is revealed in issue #5 that Raph's favorite color is red.