Although the golden age of both the Greninja and the ninja of Fuchsia City has long passed, with the advent of modern, less training-intensive methods for people to spy on and kill one another, both pokemon and human ninja are still extensively used in the criminal underworld.
This global age, however, is one where the conflicts of criminals, heroes, and politicians need not be confined to a single region, so Kalos' and Kanto's champions of espionage and assassination should finally have met in combat. Yet much had changed for both groups since the sengoku and feudal eras of their respective histories, and faced with a proud opponent who wielded similar techniques, they were too moved by respect for their mutual dishonor to fight to the death – despite the large funds which Interpol and Team Flare had offered them to do so, some of which they had paid in advance.
Instead, they used their considerable skills to fake a mutual massacre, exchanging a large number of ninja skills in the process. The techniques for steel-piercing shuriken made of water and mats which blocked all pokemon attacks were unknown in Kanto even a few years ago, yet rarely are they not mentioned today in a report (itself a formidable task to write) of the Fuchsia clan's activities. Greninja have gained less in the way of techniques, for in this day and age, trainers are always experimenting extensively with anything their pokemon could theoretically learn, and Fuchsia city poisons can not be handled by Greninja anyway. But they have made up for this through improved training, for the Greninja who lived up to their species' name had long been stubbornly wild pokemon, for the only thing a ninja pokemon can truly trust and understand as a trainer is another ninja.