The quest starts off with two guards in any hold talking to eachother asking each other if they believe the rumors about the dwemer. A new quest is started from this and you go to Morthal where you go to the dwemer museum and ask questions about the credibility of this. Just then, two archaeologists come up to you and ask for your help an expedition to dwemer ruins. Once you accept, you follow them to a ship and the real questline starts. You go to an island off the coast of Skyrim and you see the usual broken up, beaten dwemer ruins and there are some bandits guarding it, and so on. You go inside and you fight the typical dwemer spider and sphere and even a centurion. Now, this isn't the usual dwemer ruin, this one goes for a very long time, and the archaeologists you are with remark about the size. Eventually you will reach the end and at the end is a large door, made out of several feet thick metal. The door is decorated with a lot of machinery covering it, gears and levers but no way to open it. One of the archaeologists with you suggests that you go out and find some missing peaces while they stay there and try to find another way to open it. Well you go out and find a secret door leading to a room guarded by several centurions and there is a lever there. You take the lever back, plug it into a hole, and the door opens.
Inside is where things start to get very interesting. The dwemer are still alive, and they are walking around and going through life very casually. Beyond the door, the city is enormous, about the size of Solitude, Whiterun, and Morthal are mixed with eachother. It is an entire subterranean city. You see dwarves at forges, creating some automatons, shopkeepers, etc. Once your through the door, everyone stops what they are doing and stares at you. The archaeologists are stunned and make faint whimpers, and finally say how astonishing all this is. There is whispering that is exchanged through the crowd and eventually two guards, dressed up in full dwemer armor come to you and say, "We don't get many visitors, your coming with us." or something along the lines of that and tell you to follow them. You follow the guards and see more of the city, with every dwarf staring at you and then continuing with their life. A giant palace comes to view and you are forced inside where you meet the king. He comes up to you and remarks about the lack of visitors that they have seen for the past centuries, and offers for a grand feast in your honor. The meal is set up and everyone is talking and having a fun time, the king raises is glass and makes a speech and then continues eating. After a few minutes one of the archaeologists says that the world thinks your all dead, disappeared into Oblivion.
Then the entire table goes silent. There is no talking until the king summons one of the people to come up to him and he whispers something into his ear. Then, the king stands up and says to the guards, "Would you please show our guests the way out, they can't know we exist" And a bunch of dwemer guards force swords and spears into your backs, and force you out the room, into another room located on the opposite side of the castle, where they line you up and draw back bows, ready to shoot you. One of the archaeologists falls to his knees and begs for mercy. And then they shoot.
Being the wicked sick dragonborn that you are, you don't die and watch painfully as your friend's bodies are dragged out of the room. You see the king and another dwarf, dressed in military armor, talking in front of you. You overhear them talking about a possible increase of production of automatons and then you black out.
You wake up in a cell with nothing but a bed. You now need to break out of jail, and when you do, you have to sneak through the guards, and make your way out of prison and into the palace. Your plan now is to overhear more about what the king plans to do. After a bunch of sneaking and combat you make it to the castle where you see the king talking to the same guy as when you blacked out saying that the invasion on Skyrim starts the next day. After you hear this, you need to get out of the dwemer city and into Skyrim where you bring this urgent message to the lead dwemer archaeologist in Morthal and after this, he rallies up all the Holds and makes plans for defenses. Once all this is done, massive war between the dwemer and Nords of Skyrim break out. From this point on, your only goal is to assassinate the king as he has no plans or peace.
So basically what I want out of this is for you to discover the last of all the Dwemer and when they discover the world doesn't know they exist, they try to lead a surprise attack and rule all of Tamriel. Of course, the story doesn't have to go the way I imagined, but this is just a guide as to how it should go down. Please give your opinions on how this might work.