I always figured that when the Nerevarine gave Almalexia the Mazed Band, she teleported in, and tortured/killed a defiantly silent Sotha Sil.

Yet...

(This is based on a game with modded graphics, so these may have been annoyingly added and be inaccurate, and if so please let me know.)

Going through the Clockwork City, there are a lot of things that don't add up, and I half wonder if Sotha Sil was 'silent' because he was already long dead.

When 'you' first arrive the place has seen MUCH better days. It only looked slightly more well kept than some Dwemer ruins. Its even flooded. There are traps that have been activated and left active, including spikes with blood at the base, iirc. There are human bones to be found. There is even a door blown off its hinges. One of the Imperfects has had ts arm ripped off, pressumably by Almalexia, and the other seems to be in mid grab as it went 'back to sleep'.

On Sotha Sil himself he looks practically mummified.

It could be the 'graphics overhaul' added the blood at the base of traps and the bones, but broken door and the Imperfects are still there, and make me wonder why when Almalexia pressumably just teleported into his chamber. There is also no apparant accounting for the potential aging of the place. Gameplay wise its likely just foreshadowing for the players. Yet, its interesting to either imagine there were othther soldiers there that got caught in the traps, or Almalexia storing through the city and ripping it up.

Is there any other sources besides the hints we see (which in my case could be lying) and Almalexia's few words on the subject?

What makes you think Sotha Sil didn't look like that before Almalexia got there? He's hooked up to what look like wires. He's become a cyborg god, if you ask me.

He withdrew from the world entirely after the incident at Red Mountain where Dagoth Ur acquired Sunder and Keening. In the intervening centuries he allowed the city to fall into disrepair. And as Jara points out he probably looked like that well before Almalexia got there. All I think she did was break his mask and kill him.