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.