When I recently reviewed a Lovecraft-inspired anthology – Shadows Over Innsmouth – I was particularly critical of the cavalier manner in which the writers disregarded (in my opinion) the clear facts of Lovecraft's original Innsmouth tale.
(Apparently, I may be wrong! I understand the anthology has two sequels, so somebody likes it more than I do…)
For the benefit of my own sanity, I thought it would be useful to set out the facts which Lovecraft established in his original novella. If you have not read that novella, please read no further, as I will discuss things which might ruin the suspense of that story.
The Threat in 1927-1928
The original Deep Ones are from the Pacific, and were defeated by an attack by Pacific islanders aided by the Old Ones. (The 'forgotten' Old Ones have the ancient magic and know how to fight the Deep Ones, but not the power to destroy them.)
Captain Obed Marsh brought back to Innsmouth, Massachusetts, the cult of the Deep Ones from the Pacific Islands in a previus era, possibly including Deep Ones from the Pacific, and then makes contact with a conveniently located Deep One city in the depths beyond the Innsmouth reefs: Y'ha-nthlei. We're given to understand that the Deep Ones cannot easily be stopped in New England, as there are no Old Ones in New England with the proper knowledge. They have infested Innsmouth (apparently through both conversions and breeding with humans), carry on some limited forms of commerce, and openly practice worship of Dagon.
The protagonist of the story tips the authorities to what is going on at Innsmouth, and in the winter of 1927-28, the Federal government raids the city under the cover of a crackdown on bootleg liquor. This seems to involve police agencies as well as the Army and Navy, and suggests that the United States government has secret knowledge about the Deep Ones.
Note, however, that the U.S. defeats the Innsmouth threat through brute force rather than arcane knowledge: the dynamiting of the harbor buildings and tunnels in the city, and the firing of torpedoes into the depths of the ocean. However, Y'ha-nthlei is hurt, not destroyed.
Whence the Deep Ones?
The Deep Ones are some combination of fish and frog, and are worshipers of the Great Cthulhu and the fish-god Dagon. Their ultimate motive is to receive the ancient tribute owed to Cthulhu: human sacrifice.
While we know that there are other Deep One cities, we're given nothing to believe they have any political structure above city level.
Some Deep Ones are motivated to live among men, and even to procreate with mankind – it's never clear why. We're told that an 80,000-year-old Deep One is forced upon Obed Marsh as a wife, and with some difficulties conceives a hybrid daughter. Some of the hybrid descendants acquire the 'Innsmouth look' (particularly staring, fishy eyes) as they age, and eventually mutate to an inhuman state before being compelled to join the Deep Ones in the ocean depths. The typical hybrid is low energy and low intelligence; only their leaders show drive and personality.
Despite being followers of Cthulhu, the Deep Ones seem to have some good qualities: they live an eternal, dream-like existence in their underwater palaces and gardens. Though they have an evil purpose, they are often content to let the years pass by as they 'rest'. Their activities among mankind are often directed by their hybrid children.
The Deep Ones plan to 'rise again' to a city greater than Innsmouth next time, and have 'brought up' from some greater depths suitable resources (including the dread Shuggoths). They plan to spread among mankind, but it is not clear if they will use covert or overt means this time.
Continuing Beyond Innsmouth
If I were to plan a post-Innsmouth campaign, I would move the action to a major city: Boston, Hartford, or New York City would make great targets.
I would have to decide what course the Deep Ones have chosen: are they once again infiltrating among mankind, and have they found more subtle means? Or are they moving their forces into position to make full-out war?
I think I would also have to make some decisions about how leadership works among the Deep Ones, and what motivates their desire to mate with humans. And on the other hand, just how much does the U.S. know about the threat?