Dr McNinja is from an ancient irish clan of ninjas, but ammended that life style with a medical degree in nearly every field, and created a successful medical practice. As a self-proclaimed former member of the League of Shadows, he self-proclaims that he trained under Batman. Batman has said that this is a lie.
Dr McNinja's receptionist is a Gorilla named Judy. She knows sign language, and takes care of all of the doctor's appointments. She also speaks in sign language, to no avail with her non-signing boss, Dr McNinja.
Pirates vs. Ninjas
This is a real and ongoing conflict which dates back to the formation of the McNinja clan. Their village was attacked by pirates, but they resisted by demonstrating a genetic predisposition to ninjutsu through their fighting style and by instinctively picking up frozen shamrocks to apply them as shurikens. A passing ninja observed this, and taught them the arts of ninjutsu.
Law of Conservation of Ninjutsu
According to the "inverse ninja law" one ninja is an unstoppable force, whilst a horde of ninjas is just cannon fodder for one heroic foe. One of Mr McNinja's fiercest foes, the 80's-movie martial artist Frans Reyner uses this to his advantage when releasing a horde of Dr. McNinja clones to make the original a faceless and easily beatable 'stormtrooper' in the crowd. The advantage is cancelled out when Dr. McNinja conforms to the trope laws and pairs up with Frans (against the villain's will) to form a dynamic fighting duo. This allows Dr. McNinja to survive (by killing his own clones) until only he and Frans are left, which again makes him an individual ninja and thus unbeatable.
The existence of dinosaurs
Dinosaurs are not extinct, but still alive and thriving on a remote island owned by Rupert Murdoch and a deserted, Pacific island housing the ruins of an old Amerindian civilization. Also, when Earth was hit by the meteor that killed off most of the original dinosaur population, some of them were flung into space and exposed to "space radiation" which allowed them to live until they crashlanded on another planet, and develop human-level intelligence. There are at least two timelines where the dinosaurs have returned to Earth and subjugated the human race, having become infuriated by our usage of fossil fuels.