The stranger took the rock and quietly, so as not to wake Jon, wished for an exact copy of the stone for themselves.
After a quick test to ensure it worked, the stranger pocketed their own stone.
Then they chose to make a wish on Jon's copy of the rock to transform it into something else. Something that wasn't small and wasn't convenient to use. Even better, something that would be embarrassing for him to use. And best of all, it couldn't be reversed so Jon would be stuck with the ex-rock in its new form (even if he figured out there was something wrong in the first place).
Softly, the stranger whispered into Jon's rock, "I wish this stone and only this stone...
