...Different Destinations - S3-E5
Trivia: While they're waiting for the Venek Horde to attack again, when John's chained to the statue Scorpius/Harvey's playing the harmonica with his feet up on John's lap. Notice that both soles of Scorpius/Harvey's red boots have the name "Andy" written on them. In "Toy Story" Woody's boot has "Andy" written on its sole, and here in John's mind it's to signify John's ownership of the neural clone.
Trivia: One of the girls in Wayne's Missing Children's files is Annie, Clayface's split-off clone from The New Batman Adventures episode "Growing Pains".