The ninja is from early in the development of FEZ. Ninja does not appear in the final version of the game.
"I sort of remember Phil talking about how the 'ninja' should pop in sometimes in cutscenes as you play and hint at another, faster, more knowledgable and alive character that is still exploring the world, but I can see why it's been dropped... FEZ is all about lonely exploration. Adding a twist like that kills the feeling. [...]" - Renaud Bédard