I think I found out what has a hold on Soren. I've been doing some research, and I'm fairly sure it's something called the Manufactured Newborn.
And before one of you snarky commenters remarks that I could have google searched for it:
A. How do you search for a monster machine? There's thousands of those (on the internet, anyways).
B. I don't have internet all the time. Why do you think I only update this like every twenty years?
Anyways, the Puppets have vanished completely, which, I will admit, has sort of thrown me for a loop. I assumed they'd hang out and fight again, but I guess not. I did, however, find something kinda disturbing: remember the industrial center where we fought the Prophet, almost a year ago? The steel plant? I went back. That was where some dimensional bleeding happened, and I think the same force is at work with Soren.
I spent about two weeks staking it out, then moved in. I found the same place, and I found out that it wasn't an isolated incident. There's marks along the walls, drawn in invisible ink. Most of them are gears/chains of some sort, though I saw an Operator symbol in there, as if it was drawn over the gears to deface them. I stopped looking once I saw it for about fifteen minutes, just in case it drew the Operator's attention. Luckily for me, it didn't, so I went back to looking. I'm fairly sure there's an equation detailing when the portal opens, but it's going to take me some time to figure it out. I'll post when I finish it.