In 2012, Jinichi Kawakami emerged as the last surviving ninja grandmaster. Kawakami believed that the art of ninjutsu has no place in the modern age, as we have better weapons, the internet, and better medicines. Masaaki Hatsumi, another surviving ninja grandmaster, has not appointed an heir. Once Kawakami and Hatsumi pass away, ninjas will forever cease to exist.
Can’t the two of them just reproduce? Granted, I’m not a ninja scientist, but I think that’s how it works.