I spent a great deal of time finishing jobs for Vex and Delvin, having heard about "Restoring The Thieves Guild To It's Former Glory", often repeating cities far more than necessary to improve my skills. It got to a point where I had completed all four cities and the special jobs and I just kept going until I realized I've counted over five quests but it was no longer progressing.
So I figured this was a bug where it required console commands to fix, and I did. I reset the chain of the Thieves Guild quests, which triggered my chance to be able to speak to Brynjolf. This appeared to have fixed my position in the Thieves Guild, but during the ceremony, I noticed a new member Karliah… I figured she was just another new recruit who was to be added during my progression in Restoring the Thieves Guild so I didn't think much of it. I had already spoken with the new members as I did my way with Vex and Delvin, and Karliah had no special dialogue so I thought she wasn't essential.
Later on (much later on), I came across something about "Twilight Sepulcher" and found the location. Looking further into this, I learned that this was to be part of a quest from the Thieves Guild which involved Karliah and Mercer Frey. Mercer never provided any dialogues and his impatient attitude left me to dislike him so I never bothered with him. But now I'm in this mess where I can't find Karliah and Mercer just disappeared after the console command fix… Furthermore I learned that I was supposed to explore with Mercer and find Karliah (or something like that).
Was I supposed to speak with Mercer instead of Brynjolf? Was I supposed to come across Karliah during these quests? Did I just skip an entire quest line? Did I break my game?
I'm not much for posting Q&A or the like but this feels like an ugly game-breaking mess to the point where I don't even know what to ask and found no similar posts.
Best Answer
I’m not sure from your description which quests you’ve done, but the only way forward after using the console to change your position in a large questline is to use the console some more.
You can find a list of Thieves Guild quests at UESP. Start out by noting which quests you’ve finished and which ones you want to do. It sounds like none of the remaining quests are going to start by themselves, but you can hopefully get them to start using console commands. You may need to check the list of commands at both UESP and The Elder Scrolls Wiki, because the list of commands on each site is incomplete.
It looks like you were supposed to meet Karliah during the Speaking with Silence quest. That quest may be difficult to fix at this point, but you might be able to skip it by finishing that quest in the console and forcing The Pursuit to start.
At minimum, you can explore Snow Veil Sanctum (the location for Speaking with Silence) simply by unlocking the door with the console. I did that without joining the Thieves Guild and it worked fine, except for a part at the end where Karliah was supposed to be there, but she wasn’t.
For more specific advice, I think we’d need to know which quests you’ve finished, what console command you ran, and what quest or dialog you’re trying to activate. You can hopefully get a lot of the rest of the questline to work, but it may take a lot of editing from the console.
One thing you could try is to move yourself to Mercer’s location and see where he is:
Perhaps he’s waiting for you in a quest location somewhere, and has some dialog that could advance your progress. If you use that command but don’t see Mercer anywhere, he might be deactivated. You could re-enable him, but I don’t know if that would make things better or worse for your quest progress:
Also, I suggest keeping a lot of saved games, so you can back up if the console commands you try make things worse.