In the first pages of the shadow over Innsmouth its explained how, after the raid, the civil rights movement started a short-lived campaign against the gravely unconstitutional actions of the federal government (illegal arrests of American citizens, imprisonments without judgement, etc). 

The solution of the government was simple: they took some civil right crusaders and journalists to visit a few prisons where Deep Ones and hybrids were jailed (perhaps the Ice Cave?). After that, they agreed to keep Innsmouth in silence (probably a few veiled menaces from Hoover helped).

Now imagine that one of the journalists (let's call him Nathan Cullen), was "deeply" disturbed by what he found in the Arizona prision and started a private search about what Innsmouth was really about. Cullen talked with some of the few Innsmouth human neighbours who came back to the town after the raid, explored the church of the Esoteric Order of Dagon, etc. He even interviewed Robert Olmstead, the protagonist of "The Shadow over Insmouth", and was shocked to see how Olmstead has starting to become a Deep One. Olmstead also showed him the gold artifacts that he inherited from his family.

Nobody could resist all those revelations and keeps his sanity intact: Cullen stoped his research and started drinking heavily. Due to whisky, he lost some of his credibility as a journalist. And finally he commited suicide when he was fired from his job after being included in McCarthy "Black List" in 1951.

In 1998 a young political sciences student (let's call him Henry Mateoti) starts his thesis about Mac Carthy's victims. Searching in Arkham University archives, he finds Nathan Cullen diary and is amazed to discover that the worst federal attack to the civil rights since Wounded Knee (the Insmouth Raid) had been kept in silence for almost 70 years. Perhaps Mateoti should had finished reading the diaries before changing his thesis' objective.

Mateoti is somewhat innocent and idealistic. He thinks that Insmouth neighbours were discriminated by being from a different race (Polynesian) and religion. He starts asking questions in Innsmouth (searching parents of the raid victims), FBI and Arkham and Boston newspapers.

At least two groups would be interested in Mateoti:

First of all, Delta Green: one of his raisons d'etre is keeping the Mythos away from headlines. They must convince Mateoti that Cullen's diary is only a product of delirium tremens and erase all the files. Remember Delta Green lost most of its Insmouth treasures in the 60s.

Second of all, the remains of the Esoteric Order of Dagon: some hybrids (especially those who didn't show the Innsmouth look) fled from the Marines. They lost the priests, the sacred books and the ancient knowledge during the Raid. Also, nowadays the Deep Ones don't answer the summoning spells. These hybrids who have survived in ruined Insmouth, are now highly paranoid about being hunted by the feds. When Mateoti appears and starts talking aboult Olmstead, Cullen, the Arizona prison, etc, they at last see a light: Mateoti will show them a way to recover Olmstead's relics and to free their lost brothers in jail. Once freed, they will all find the way back to the sea.