"5: Some Deep, Organizing Power..."
We see in flashback a cliff-side duel between Sherlock Holmes and James Moriarty, where supposedly both met their deaths, but we learn that Moriarty did not die, and that Moriarty was a double agent in the British Secret Service.
Jump to the present, and we see that the returned compound is to be used by Moriarty in his campaign against his rival crime lord, the Devil Doctor of Limehouse. The Invisible Man, however, brings this secret back to the team, who realize their error, perhaps too late. Moriarty's war ship hovers over the East side of London, ready to wipe out it's rival and the League in one assault.
"Allan and the Sundered Veil, Chapter V: The Glint in Fortune's Eye"