It's a blood stone in Pontius Pirate's chest on the ship. That's the one the orcs and pirates are talking about.
... but that chest did not have a stone in it. I even went back and checked again and the chest is empty.
Maybe I'm miscounting something. The locations I have unlocked at The End of Time is the telescope and Hero Hall. There is another gate that is active, but for some reason I can't use it.