I've ran into a bit of a problem with a quest in Markarth called "The Forsworn Conspiracy". I've found evidence against Nepos, talked to Margret and found evidence against Thonar. Upon returning to Eltrys I'm meet by two guards, and one called Legate Emmanuel Admand. Eltrys is dead, and for some reason I have a 40 gold bounty.
However the quest does not update, from searching around some I get the feeling I'm at this point supposed to finish the Forsworn Conspiracy and get a quest called "No One Escapes Cidhnna" as I'm sent down there, however this doesn't happen. If I pay the fine, bribe the guard or persuade my way out of the situation nothing at all happens. If I go to jail, I am sent there but without getting this quest, making it impossible to break out of the jail and worse impossible to progress in the quest because this is supposed to bring me to Madanach. There are only two doors, one even impossible to interact with entirely, the other only possible to open with a key. Which I understand the orc should open for me if I had the appropriate quest start.

All I can do now is buy a weapon with skooma, then I'm stuck, forced to mine veins to serve my time. Any way around this? Unfortunately I have no recent enough saves since before entering the area where Eltrys lies dead. I've tried to use "unlock" on the door through the console which allowed me to enter. Though unable to interract with Madanach, even killing him had no effect.

Strange - have you already had the scene where Thonar's wife is killed?

Yes, that has already happened. One thing though, which may have made a difference, though the quest should've handled it considering dialogs and everything seemed to be made for it to be a viable option, but the woman at the start was never killed. I killed the guy before he got the chance

I don't know if this matters, but did you kill Thonar? He was still alive when I went back to meet with Eltrys and then was jailed.

probably a silly question, but did you talk to the orc?

No, Thonar still lives.
Is there any console command which can force complete an objective or quest, or maybe force start the other quest? I know this may potentially bug it up worse. But just making a save and trying, got nothing to lose since this quest is already broken

ok, incase someone have similar problems with this questline.

Typing "Setstage ms01 100" Will complete the quest, teleport you to prison and starting the followup quest. I've had a problem with spawning in the starting place without the guard to let you into the actual prison when using this method, but the door can be forced open with the "unlock" command, thus allowing you to enter, or use the teleport to questgiver to get inside.

Alternatively, and possibly better, go to the guards. Get arrested as usual, she'll open the door for you and the quest will be bugged, then type in "Setstage ms01 100", making you jump back into the 'spawn point' but the door should still be open so you can run through and get inside.

As always when using console like this, should be a last resort, and can always create bugs further in. My advice, make a backup save before doing it and after completing the entire chain of quests try to communicate with as much of the involved characters afterwards and check with guards etc. Just to try to ensure that there is no bugs lingering from it.