I just read the book The Great War in Skyrim.
It mentions a period of two years where Masser and Secunda vanished. What could that possibly mean? It seems to be literal, that the moons actually disappeared.

The Khajiit were terrified, and when the moons re-appeared the Thalmor took credit for it. Therein lies the question - what could have caused them to disappear in the first place? Could the Thalmor have been behind that? Magic is a strange thing indeed.

It seems to me that it would be far easier to mask the moons for a few years to scare the Khajiit and "bring them back" by stopping whatever magic you had used to hide them, than it would be to try and find/replace/repair moons that had actually vanished of their own accord. Besides, it would be the perfect way to curry favor with a superstitious province of the Empire. Or are the moons of Nirn prone to vanishing from time to time?

The moons literally vanished from the sky for two years. This period of time has come to be known as the Void Nights.

No one really knows how or why the moons disappeared, nor does anyone really know how or why they came back.

This is how the Thalmor gained their stranglehold of influence in Elsweyr. When the Moons returned (4E100), the Thalmor took credit by stating they had used previously undiscovered "Dawn Magic" to restore the moons. Obviously, given Khajiit's cultural ties with the moons, and how important it is to them as a species, such a claim had the Khajiit praising the Thalmor. Eventually all Imperial influence in Elsweyr had diminished, and the Aldmeri Dominion sundered Elsweyr into the ancient kingdoms of Paletine and Anequina.

Yea. It's a clever way to gain favor in Elsweyer.

The real mystery, and I don't know if some lorebuffs on these boards would have better knowledge, is this:

Did the moons:

• Disappear and Reappear naturally (Nature/Nature)
  
• Disappear by the Thalmor and Reappear by the Thalmor (Thalmor/Thalmor)
  
• Disappear naturally and reappear by the Thalmore (Nature/Thalmor), or
  
• Disappear by the Thalmor and Reappear naturally (Thalmor/Nature)

Any of them could have similar political motivations. In the first one, the Thalmor just capitalize on a crazy lucky and strange event. In that case, what did cause it?

In the second, the entire situation was engineered by the Thalmor.

In the third, the thalmor did what they claimed to do, and brought the moons back after a mysterious disappearance.

In the fourth, a Thalmor plot to throw Elseweyer into dissaray worked, but not entirely. They could not sustain the moons' disappearance (or someone/thing else brought them back). Again, the Thalmor would then just capitalize on it and take credit for them coming back.

Given that the Moons of Nirn are considered both Celestial Bodies, and Flesh Divinity of a fallen god, the possibilities are endless. It could be something as simple as a the orbit of both Masser and Secunda being in such an alignment as to create a nearly-pepetual lunar eclipse, and simple astrological observations (The kind the Dwemer were known to do) could verify and predict these events.

It could be something a lot more "Mystical". Maybe Lorkhan is protesting the removal of mysticism by showing it's power?

The moons are the body of Lorkhan and integral to the Mundus.
It is completely unknown what their dissapearance means but I think we can rule out any natural events.

It hasnt happened any time before and it doesnt make sense for the body of the arguably most important god to vanish.

The Thalmor however are trying to do something to the stability of the world.
By removing the mythical awareness of Talos, who is the mirror-brother of Lorkhan, they believe they can unravel creation itself.
I believe that the dissapearance of Lorkhan from the night sky and his subsequent return as foretold by the Thalmor indicates that it is a part of their machinations.

It was some sort of experiment. Thalmor were messing with stuff, made the moons disappear (part-accident, part-intention), and then tried to figure out what they did and how they did it, and once they understood, they brought the moons back. Perhaps they might have greater plans in store for the future, but I'd prefer to think they probably didn't see much usefulness in it (they were probably expecting something big to happen when they got rid of the moons, like mankind to disappear or for creation to unravel). When nothing changed, they brought the moons back. Experiment failure for the Thalmor Magicientists. But then a cunning Thalmor politician said "Hey...we could use this to manipulate the Khajiit..."

The scariest antagonist is the one of which you do not understand the powers and limitations. I'm not sure I want to know whether it was the Thalmor who killed the moons. Better to wonder, and to fear.

If they can erase Lorkhan from the sky...what is safe? No, surely, they couldn't do such a thing. Surely?

Maybe it was just the Psijics?

Crack theory: The disabling of White-Gold shook up the foundations of the Mundus so much that the moons disappeared. They reappeared when Talos got Mundus's [NUMINIT] together.

Where were you When the Moons Disappeared?

Well, that's just the thing, isn't it? The Thalmor discovered that by simply removing Lorkhan they could not undo his creation. Why? Because someone else was holding creation up. Someone unexpected. Perhaps that's the moment when war against the Empire was inevitable as a part of their goal. And why they pressed for the elimination of Talos worship as terms.

I have no idea why they wanted Hammerfell so much though. That's another topic, but it did seem to be a primary objective for the war, didn't it?

In a universe where deities and demons actually take part in the lives of their adherents, what is a "natural" event or cause?

One that isn't caused by the adherents.

M'aiq knows. But he won't tell you.

I like this idea the most, but I think I can answer part #2; it's a foothold onto Tamriel.

Remember, the Thalmor are all the way on another island, and they lost the support of the Psijics. In order to be able to move relatively safely onto Tamriel, other than going through Valenwood, would mean going through Hammerfell. The Imperial Navy would likely surround Anvil, making it a poor place to just attack. Better to go other route. In short, militarily advantageous locations.

J'derras believes the Thalmor were to blame for the disappearance of the Moons. It is far too suspicious to cast away the high probability that the Thalmor were responsible. They ARE mages after all. They kinda remind me of the Red Wizards of Thay from Forgotten Realms. Maybe they have some form of circle magic that would allow them to pool their magic into a single powerful spell that could conceivably cast invisibility on the moons, much like that one mage in Oblivion (names fail me) who turned an entire village invisible for an indeterminate amount of time (it was weeks that past before the CoC broke out of prison), and that was just one mage.

I still haven't learned what happened to the Khajiit, as far as I'm not totally confusing stuff right now, the moons control what kind of cat a newborn Khajiit is going to be. Since there were no moons, did they give birth at all?

I have never heard anything about that matter.

The Thalmor can't be behind everything.

Or can they?

Of course they aren't. They weren't behind the reappearance of the dragons. The argument is whether or not they are behind this specific event.

My guess? Thalmor trickery to get Elsweyr on their side.

Sometimes they're upfront.

They're mostly bystanders, really. They're just taking advantage of all these horrible events to further their cause. All they've ever directly done was the Great War and the Concordat.