I was leaving the dark elf village and Virgil left like he was supposed to. I went to the Sobbing Onion and into the trap door to find that Virgil was not there. I have tried going back down there and waiting down there. Going during night and during day, but Virgil is just a no show. What is going on?
What is your game version? I recall reading that sometimes Virgil can get "stuck" while running into the woods after T'sen Ang, which prevents him from appearing later in the Sobbing Onion. If this is what happened to you, from what I remember there is, sadly, no way to fix it. No way other than reloading right before leaving T'sen Ang and trying again, that is.
I now have the version downloaded from Drog. This is actually the second issue I have had with this. The first problem I encountered with it, Virgil never left the group. Somehow I skipped him leaving and he just stayed with me. I think he may have died and when I resurrected him I had walked past the point that he stops you to tell you he was leaving. He eventually left later when engaging conversation with him. I don't think he came back either time. I deleted the game files and this happened a few weeks ago. Sorry for the lack of memory. It may have been him getting stuck both times and unable to travel back to the Sobbing Onion. I will repost if I encounter this problem again. Thanks for the advice Muro.
Happened to me on my last play through I flew in to rescue virgil from the gangsters but he was nowhere to be found so I just killed the gangsters and left and slept a bit came back and elder joachim and virgil were there.