"Nintendo Ninjas" is the colloquialism for employees of Nintendo's legal department that work to protect Nintendo's intellectual property. These agents have taken down fan-games, disrupted the work of people distributing modified Nintendo hardware or software, and have, most importantly, worked extensively to suppress information about the Personalization A.I. and Super Mario 64 anomalies. It has been rumored that these agents have gone to extreme lengths to conceal the true nature of Super Mario 64.
The efforts of the Nintendo Ninjas are believed to part of the reason that Super Mario 64's anomalies were not discovered until recently, as they were previously successful in covering up information about the anomalies and the A.I.. It is currently unclear as to why the Nintendo Ninjas have seemingly stopped covering up Super Mario 64's anomalies.
Strange people believed to be Nintendo Ninjas have been reported during events where versions of Super Mario 64 with the AI were present; such as Spaceworld 1995, speedrunning competitions, etc. These people were said to loiter while observing people playing the game. It is currently believed that the Nintendo Ninjas were present at these occasions incase any anomalies in the games were encountered and to suppress information of these anomalies if they did manifest.
Several people who have reported anomalies have also reported seeing conspicuous individuals repeatedly, believed to be Nintendo Ninjas stalking them. In most cases, these reporters have stopped communication shortly after reporting those occurrences.