After crash-landing on Shonenia, Andrew and Elly somehow escaped the planet in a brand new ship. Andrew seemingly had no idea how they got it or where it came from, although he was awake and well when Elly regained conciousness from her ordeal on Shonenia.
Presumably (not just for the sake of the joke), Andrew was able to escape with Elly from the lair and take it from the Shoenians (but we don't know that for sure). How the ship got into their possesion may become clearer in the future, but knowing Bonus Stage, don't hope on it. It was probably just a throwaway joke in reference to how Elly's scenes are almost always cut.
The Bonus Stage crew eventually used the ship to escape from Hydrox in The Day The World Did Stuff.
- Elly in Chains
- The Day The World Did Stuff