The secret monkey is the unseen antagonist of the whole series, unknown by most users the monkey i responsible for the predicament Fredrick is in.
The monkey seems to be a male chimpanzee. my theory is that the meaning of this is both for humor, and to mock the United States former president Ronald Regan, who stared in a movie with a male chimpanzee called Bedtime for Bonzo. if this is true Running Fred has a secret meaning, to protest the conservative president.
I have only been able to find one screenshot, the amount of time it took me to get this screenshot took me hours 12 if I'm honest, but now the truth is out.
Man Monkey out