I gathered 3 evidences against cardinal Trancquillius and I already got the permission to arrest him. But he just vanished. I looked everywhere for him, still cant find him. Can anyone tell me, please, where this damn bastard is?

He has gone into the lowest level of the chapel once you get permission to arrest him. A priest will now appear, approach you, fight you to the death and drop a key needed to open the locked door at the beginning of the first level underneath the chapel.

Thank you, I figured that one out after 10 more mins:)