I'm changing some elements of the module from the campaign setting it was written for to put it in another campaign setting. However, the status of the religions involved with the temple investigation remain the same, even though the names have changed.
I'll be adding some details about the module here, so there will be some spoilers. I'm attempting to hide them by changing the color of the text in this box.
Beware, spoilers.
The module is Cormyr: The Tearing of the Weave. I don't have the Forgotten Realms Campaign Setting, and we are playing in Greyhawk, so I'm making some modifications. The Temple in question is masquerading as a temple to Mystara when it is secretly (unknown to the guards and some of the clergy) serving the purpose of Shar and Cyric. I'm changing it to Boccob with secret connections to Wee Jas and the Suel.
The clerics, secretly evil, have undetectable alignment potions so that they appear to be not evil. The cleric in charge of public relations has an obscene bluff check bonus of +15, so the party has been unable to find any reason to distrust him except for the suspicions of a real priest of Boccob who's very nervous about the temple.
The false temple has a ritual to dominate people who visit the inner temple. The party's cleric (who led the attack on the temple) and the sorcerer participated in this ritual to try to get more information. The sorcerer voluntarily failed his Will save to be dominated, thinking he would gain greater magical power. The cleric was unaffected because he had a Protection from Evil cast on himself during the ritual, which so happened to block the domination effect. The cleric did not however, in game, know that this happened and that the sorcerer was dominated. To his knowledge he just did not "get" the ritual and was sent on his way.
So the party is actually doing the "right" thing, but they are going about it in a reckless way. Had the paladin and fighter not left to get the guards, there wouldn't have been a stink raised locally soon enough. The group would have gotten inside and found the evidence they need to prove that evil is going on. But as it is now, betrayed by the forces of law and good, the party can't reasonably get inside the temple.
I did email my gaming group, explained to them the situation going on in the city with the town guard. I'm asking them how they think we should proceed. I'm tempted, just to spare inter-party conflict and hurt feelings, to do a reset on the campaign.
Retreater