A mysterious doctor has arrived in Ratbridge touting 'Black Jollop'; a wonder cure for all ills. As the townsfolk flock to the doc, Arthur's grandfather is one of the first to take the medicine, but disaster strikes when supplies run out. Meanwhile, the Nautical Laundry has money troubles. Without drastic action the band of rats and pirates who live on the ship won't stay afloat. So when the doctor offers a princely sum for a far away voyage to gather ingredients for his cure, the crew jumps at the chance to save their ship. Accompanying them are Marjorie the inventor and Willbury Nibble. Unbeknown to them, Arthur has stowed away with his friend Fish, the boxtroll. And a good job too, because a nasty surprise is afoot when the new captain is revealed as an old enemy, along with the truth about the disastrous side effect of the medicine... and it all comes down to one thing: CHEESE! It's up to Arthur and Fish to save the crew and find the antidote. But first they have to get past the monster guarding the island...