Well, the team wanted to add a secret character, so a ninja pallet swap was the only thing they could do. That’s how Reptile got the costume.

Storywise, we don’t really know. It’s a fact though that Zaterrean people/creatures were skilled fighters, so maybe they had their own “ninja” clans and all that.

reptile got it because he 1)had ninja skillz 2)needed to blend in with earthlings 3) palette swapping is easier than making an individual character