What's going on:
A new cult of Cthulhu has formed, in a radically different form than previous cults. It is a loose commune of loners, artists, and madmen touched by Cthulhu's psychic dreams but have no physical connection to the deep ones. They have been practicing human sacrifice for years and live above the ruins of an ancient Deep one city but millions of years have changed the sea to the desert. A social worker discovered their practices and paid with his life. The DG friendly discovered the shallow burial ground of a corpse and was shot by a paranoid cultist shortly afterwards.

This cult of Cthulhu has few connections to the old cults except through the dreams. They have no connection to modern oceans, deep ones or Innsmouth. They live in a desert and don't think of themselves as cultists. There is no central leader and their ideology varies greatly between members.
People visiting the commune will notice that the members are just talking amongst themselves, perhaps arguing about the details of a shared dream. They're not hiding anything; to them it's completely normal. Those who look at them funny while they talk amongst themselves in public are sneered at as "normals". The locals hang out in New Age shops. They are interested in crystals, incense, things of that ilk, but nothing as concrete as wicca, satanism, et. al. Any nonsense by Crowley is right out. It's not that they believe in any of that New Age crap; they're just trying to change the light they see to match the dream and get the smells right.

History:
In the mid 1980s, an unknown experimental artist was touched by Cthulhu and created several videos of his dream, 9 hours altogether. The artist committed suicide and the tapes landed in the archives of a cable tv station unlabeled and forgotten. Several years later, a broadcast engineer discovered them and became obsessed with the imagery. The engineer was fired for unstable behavior and shortly afterwards pirated the signal of several TV stations. He broadcast several segments of the footage. This in turn made hundreds of viewers susceptible to Cthulhu's dreams. Eventually a small group of them met with the engineer, who eagerly made copies of the footage
and the cult was born.

Ideology of the cult:
The cult believes the images of R'yleh in the footage is actually a utopia that can only be found through astrology, meditation and finding the lost city of atlantis. Each cult member and family has a slightly different belief system but they view Cthulhu as a transcendental god. They have no knowledge of the deep ones.

Cell A's notice:
Cell A can be alterted to the case through reports of Strange corpses, Lots of reports of excited delirium, extreme violence but without firearms ( fists, biting, perhaps clubs... but animalistic violence ), apparent rates of psychosis far above the norms for the area ( perhaps blamed on "some new drug craze") or Odd environmental events.

Hooks:

• An email from a local LEO explaining the rise in drug related violence without finding any drugs.

• A note from a local health department explaining the very high rates of psychosis without apparent cause, and that a number of affected persons seem to share the same delusions without knowing each other.

• Perhaps throw in an autopsy report... something where a bystander was killed by a cultist using fists and teeth.

• Interviews with witnesses / relatives point to the victims mentioning a strange TV show. All relate the victims obsession with the broadcast, which should lead to the engineer.

How to take down the cult:
The commune is far enough out that line power doesn't reach, so the cult uses propane. With a large supply of propane on site ( at least a few tanks ), a well placed shot from an incendiary round will do wonders. Note that incendiary rounds are available online; doesn't have to be military *cough*surplus*cough*.

Either way, let the agents observe the set up. A lot will depend on the cultists themselves. If it's a collection of RVs in the middle of nowhere ( basically camping ) then get the Agent with the highest Rifle skill a designated marksman rifle. If necessary, press a hunting rifle with scope into service. Wound / kill as many cultists as possible from a distance, then close. Finish them off with pistol shots. Leave the weapons at the scene and torch the lot with gasoline and road flares.

For cover up, leave boxes of sudafed, engine starting fluid and ether at the scene. Make it look like meth heads gone wild. If the cops buy the simple answer, you won't even need to usurp the local investigation by agents/friendlies in the BATF and/or DEA to enable a cover up.

If there's a more permanent structure, things get more interesting. Again, look for large quantities of fuel / chemicals on site. They make for lovely "accidents".

If the agents have to torch a structure and there isn't a good source of chemicals on site, they could pick up some liquid paraffin ( aka lamp oil ). The stuff burns very clean... clean enough that some g-spec chromatographs wont pick it up. Pool the stuff in corners near electrical outlets and LEOs might presume an electrical fire. There's also the lit cigarette in a pile of papers or knocked over candle as reasons for a fire, of course.

No matter the situation, the cover up should hit the high points:

• Drugs involved. Particularly meth, as "violent meth head" is writ large in the public conscience these days.

• The cultists had some sort of argument and killed each other.

• Fire resulted from the argument.

The fire is important to destroy evidence. A rifle shot from a distance ( for instance ) will leave blood spatter evidence different from, say, a slit throat. While cultists out in the desert wont likely be investigated for a while, leaving such evidence around is an invitation for a Keeper to have some fun.

The only problem is that the cultists are not centrally organized. Since there's no central leader that makes them consolidate resources, it will be more like taking down a dozen different groups each with different weapons and resources and close enough to each other that taking one group down alerts the others. Taking one of them leads to chaos which both has advantages and disadvantages. While the cultists will be disorganized, there's no one power source or building to take down. And unlike most disorganized groups, they're totally fearless and will fight to the death. Furthermore, they're unpredictable which is a nightmare for planning.

Instead of a forensically sterile site, Agents should leave evidence which misdirects the investigation.

Examples:

• Wallet and watch missing? Mugging gone wrong.

• Baggie of baking soda or catnip found at the scene? Drug deal gone wrong.

• Cultist a delivery person? Scrawl "you're next, bitch" on the package to be delivered.

• Another is to use overkill; shoot / stab / slice the face of the victim repeatedly. Make it look personal.

• As black holes were discovered by the absence of light, your point about forensically sterile scenes is well taken.