In Eclipse and the Officer X Factor, it rained, but both times it was pretty much the penguins' fault that it rained. They forced it to in Eclipse, and something about the popcorn hitting the clouds in the Officer X Factor.
Kowalski: "It's the salt! The sodium granules released from the pretzel gari into the convective wingu layer must have sparked a freezing nucleation reaction! And 'Boom!' instant rain."