Molag Bal, Dagoth Ur, Mehrunes Dagon, and Alduin are not subtle villains, even when their not encountered until the very end. I've been wondering though, could Elder Scrolls work with a villain who's more sneaky, conniving and quiet? Someone who's actions are harder to find, or may seem ordinary at first until you look closer.
Let's say that the plot of 6 is similar to the plot of the Sherlock Holmes story, The Adventure of the Dancing Men. The plot of that is kicked off when a married couple find a series of childlike drawings of dancing men (hence the title) in their garden. To most people, these drawings would be little more then art from children. But the dancing men frighten the wife who becomes scared and paranoid. When her husband brings this to Holmes, he correctly deduces that the dancing men are in fact a hidden message. The husband also reveals that his wife is from America, and that she claimed she had tired of her home country and left. But upon further investigation and deduction, Holmes learns that she didn't leave America because she was tired of it. She was trying to get away from someone or something, and her dark past has followed her to England to haunt her.
This plot could do well in 6 if it's set in Hammerfell. So much of Yokuda's history has been lost, and most modern day Redguards have only vague knowledge of why their ancestors left their sunken homeland, or why it sank. Well, let's say the main plot of 6 kicks off when you and a fellow NPC(maybe another prisoner), find a tablet with a series of strange images or symbols. To you, this is just gibberish, but the NPC, who is a Redguard is so frightened by this, they die of fear. You bring this to a important NPC character, and after some decoding, even they are frightened by it. As the plot continues, more and more series of gibberish appear, but you soon learn that these are actually coded messages that are connected to Yokuda, and you soon learn that Yokuda had a dark and frightening history which ended when it sank. And in the time leading to it's destruction, messages appeared in Yokuda. The same messages you are finding. So history is repeating itself, and a mysterious unseen evil has returned. But can you find it or figure it out before Tamriel shares Yokuda's fate?
Ultimately, you don't learn about who or what this evil is until the end, and until then, it manifests it's power is subtle, but fearful and frightening ways, and sometimes you can feel it's presence.