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Hello Kovi, (or anyone else who can help me out),
I am sorry to bug you again, but I am really stuck in this game and I don't know how to progress. I'm not sure if I'm just doing something wrong, or else there might be a glitch where something is supposed to happen and doesn't, (like when Thintan didn't appear and I had to type a code to access him).

I am currently a paladin in Act II. I have explored all the dungeons, (that I know of), cleared out all the areas, and completed almost all of the side quests. I had the four heretics burned, (Alphonso DiCerbio, Ethian De Pasque, Raimond Ventano, and Duchess Yulliette Heidrick). I even helped Robert Heidrick get remarried after I toasted his wife at the stake. I cleared the devil's caverns, sanctified the Pagan Temple with holy water, rescued Tom Clifford, killed Istwan De Bragho using holy Water, exorcised the possessed girl, and retrieved the Chalice of Metomorphosis.

So now I had Thintan retrieve the incriminating letters from Truncquillius for me, thus proving is guilt. Now that I actually have the letters, common sense dictates that it should provide the proof I need to have Truncquillius arrested, but when I go to Welfhar in the Glatzburg church to get an arrest warrant, no option to arrest him is presented to me. Furthermore, when I go to talk to Truncquillius about it, he doesn't even mention it. All he does is tell me that he can't currently disclose any details to me regarding my pending murder investigation. So I just don't know what to do from here. I've walked around everywhere and talked to everyone. I've backtracked to Act I, reread all my notes, and searched my map for a new travel point to appear......but nothing. What I need to do is have the order issued to arrest Truncquillius to advance the story, but I can't figure out how to do it.

Also, I don't know if you need to know this or not, but in my inventory, I've been hauling around the rotting corpse of some poor dead girl, a thorn apple, a sun crystal, and a foundation stone of the temple of Jesus Christ, (whom the game refers to as "the first prophet"). Am I supposed to do something with these items to make the story of the game progress? Someone told me I need to take the thorn apple to Enrie Jungwerdt to get my fortune read to me, but she never gives me that option. Any help you can provide will be very much appreciated. I am addicted to this fantastic game and really getting into the story. Thank you for your time.
I went through all of the posts on this forum and found the solution at this thread:

http://www.gog.com/forum/inquisitor/stuck_on_act_2

The incriminating letters were not enough to convict Truncquillius. I also needed the testimony of Dieter von Gelbendiel. In order to get it, I needed to make a shady deal with Dieter that I initially did not want to do since it seemed less-than-noble, and therefore out of character for the paladin that I wanted to play. Oh well, now I have to go and beat up on a bunch of evil priests in league with Satan. A paladin's work is never done.
I'm glad you found a way to get a warrant for Truncquillius yourself.

As far as your other questions go:
- You will need the corpse in Act III again - but you do not have to haul it along the whole time. You can also stash it somewhere and return for it when you need the corpse later on.
- Yes, the Thorn Apple is for Enrie Jungwirdt to read your fortune. But it seems to me that you have to ask her the right question during your very first dialogue with her to be able to open this side quest ("People say that you're a seer. That you can perceive things others cannot see. How can you explain it?").
- Sun Crystal will be needed in Act III.
- A quest for the Foundation Stone can be given to you by one of the priests in the Galibornium Temple that are sent there after you have consecrated it.