Fisicamente, uma explosão de Chemical X; psicologicamente, vivendo duro e descuidado.
Da página da Wikia (grifo meu):
During the event of the creation of the Powerpuff Girls he pushed the Professor towards a container of Chemical X, which caused an explosion, mutating his simian DNA, turning his skin green and causing his intelligence and brain to enlarge, growing out of his skull. It also gave him new emotions like envy and inferiority.
[...]
After Blossom, Bubbles and Buttercup were created, the Professor lost interest and/or attention of Mojo's existence and forgot about him. With newfound intelligence, he donned a tattered overcoat with a partially shredded scarf and a paper bag to cover his brain and ran away, setting his home up in an alley. Spending time on the street by himself with no one to care about him almost immediately turned him cold and emotionless providing a motive as to why he would care to destroy Townsville and conquer the world.
Referências: o episódio Rising do Sr. Mojo e o filme O Filme das Meninas Superpoderosas .