I was reading through 'Dark Rivals', which involves a covert war between Arkham ghouls and a witch cult. I really like how the scenario teams up the investigators with the more monstrous faction. What with the ghouls being right there, breathing down your neck, the tension is very intimate--especially since the alliance is so obviously fragile, with many opportunities for the players (or the witch cult) to muss it up. At least from reading it, the scenario seems to do a great job of making the ghouls a) just human enough to make the possibility of such an alliance convincing, and b) much more scary and interesting, precisely *because* they act a little more like human beings than in most scenarios which involve them (at least, the scenarios I've read).
I would imagine there are *tons* of scenarios in which investigators unwittingly serve evil patrons, but I feel like I haven't seen very many investigator-facing alliances with mythos monsters or cultists. I feel like there's a lot of potential there, and probably a lot of room to try out new things with well-worn monsters and tropes. How harrowing would it be to team up with a proto-shoggoth to take down a coven of elder things, rather than vice-versa? Or help unleash flying polyps so they can destroy an especially evil cult of the Great Race? I'm sure the novelty would wear off quickly if you did this more than once or twice, but it would allow the investigators to see how some of these creatures think and strategize. Handled appropriately, seeing them up close might make them *more* alien and their motives even more unfathomable.
Are there other scenarios or adventures that present tentative alliances like this? What homebrew alliances have you explored? How did your players respond to the invitation for an alliance? Or did the players proposition the mythos faction? What developments arose from the alliance that you did not expect? What happened when the alliance was no longer needed, either by one faction or both?