There's what *LOOKS* like one of those rift "emitters" in the center of the ship to the right of your start point. Since it was just a rift I simply contained it (excavated the boat to level 1 except for a cannon on the power circle from the emitter in the bottom part of the boat) and went on to finish the map, figuring the rift would go away when I got it's parent.
I cleared the map, there was nothing left but it wouldn't end. Then I noticed my Berthas were pounding that ship. The rift was still active. I finally tried placing a nullifier to kill it--yup, I could. Victory at last.