When I decided that the focus of my mod would be the introduction of two new characters to the Dark Brotherhood, I knew my mod was going to have two questlines. I could have had these two characters working together to achieve a single goal, but I knew their personalities would be very different. That would mean they would have very independent objectives. From the start Averna was designed to be the foil to Stabby's Gib. Stabby would be the silly one cracking jokes all the time, and Averna was the serious one who was busy doing creepy voodoo magicka.
These two characters had their questlines developed very differently. The philosophy behind Stabby's questline was 'addition'. Everything in his story is an addition to the existing world. He has two unique dungeons (not to mention his 'happy place') and every single character you kill in Stabby's questline is a person I have added to the existing world of Skyrim. (There is just one notable exception, more on that later)
Averna was developed with a philosophy of complementing existing assets. Almost all the virgins you kill in her quests are pre-existing characters. Her quests were an exercise in Skyrim's Radiant Story system. The first quest picks a random dungeon with hagravens that you haven't been to, sticks the Quest Objective in that dungeon and then tells the player to go get it! It was so much fun to test and debug these quests because they where different every time! Almost all of Averna's quests are driven by the Radiant Story System, I really experimented to see what clever scenarios I could concoct programatically, without having to generate any new art assets. I am after all, /* just */ a programmer.
I knew these two questlines would intertwine eventually, but it wasn't until about 4 months into production that I actually started playing both questlines at once and seeing how they interacted. That's when the headaches began. I never wanted to force the player to play the mod in a certain order or another. But I would have to set some guidelines in order to keep the system sound and my head in one piece. Fortunately the plots of both stories came to a single knot. There is only one spot where you must advance Stabby's questline before you can advance Averna's. It took a few weeks to untangle the threads into a single workable knot, but at the end of the project I was proud of how flexible I had made the game for the player.