Radioactive Ape is an ape that was exposed to radiation, causing it to glow green.
It was first mentioned in a police surveillance tape in which Ned Flanders told Chief Wiggum that Homer released the ape into his house. According to Bart, the ape tricked Homer into releasing it into Ned's house. At the end, the ape was seen repeatedly hitting Ned while he was driving. Presumably, the police were forced to return the ape to Flanders after it was discovered that Comic Book Guy had pirated the police surveillance tape and leaked it.