A human scientist based in a laboratory in the mountains outside of The City, Dr. Fongo seeks to create an army of mutant animals in order to take over the world. Why he wants to do this is not specified, nor is anything else about his backstory. All that is known is that he is very self-hating, and that he once considered going to dance school before deciding on being a scientist instead.
When GIR is hit by a van driven by Fongo's employees but walks away unharmed, they grab him and bring him back to the lab. Fongo studies GIR, and upon finding donut crumbs on him (from a snack he was having before being hit by the van) decides that donuts are the key to finally creating his mutant army. He then has GIR locked away with his other test subjects, only for the SIR Unit to accidentally inspire the other animals to rebel and escape from the lab.
Despite this setback, Fongo succeeds in creating an army of donut/ape hybrids equipped with jetpacks, which he then attacks the city with, being opposed by the escaped test subjects. A time traveler who had previously appeared to warn GIR about a horrible future ruled by apes reappears and reveals that this fight against Fongo leads to that future, and that he has to stop it by teaching both sides to dance, as dancing leads to peace.
This works, as despite Fongo's attempts to resist, he is swayed by GIR's dancing and starts dancing with the animals, stating that he finally likes himself. He is last seen dancing alongside his donut apes and the mutants through the city.