Reptile was basically confirmed to be the ninja standing behind Kotal Kahn, meaning he could be a potential ally, and based on the info for issue #3 of Mortal Kombat, I would be worried for Reptile's chances to make it into the game:

"Then, in issue #3, as the civil war in Outworld rages on, Kotal Kahn suffers an unimaginable loss and enlists the power of the Kamidogu to avenge his fallen ally. But will blood magic make Kotal powerful enough to take down Outworld’s champion? Enter: Goro!"

See; The Ninja in the comic *SPOILER*