Basically this was a theory made by FoolishOwl from the Memospore IRC channel with some of my ideas added in

The general idea is that Talos didn't actually mantle Lorkhan but rather imprisoned him somehow and usurped his position, the idea comes from the shrines of Talos in skyrim. http://bestgamewallpapers.com/files/elder-scrolls-5-skyrim/shrine-of-talos.jpg

We see Talos about to stab a snake while stepping on it now we goto a book talking about light and darkness

http://www.uesp.net/wiki/Lore:The_Light_and_the_Dark

In the story the old man is telling his grandkids about a great battle between two entities, one being of light which is viewed as a bird while the other is darkness which is a snake now the idea may come as Anu and Padomay but what if the Bird and Snake are really Akatosh and Lorkhan? Akatosh being the bird and Lorkhan being a snake what further convinced us to believe that Lorkhan was the snake is that in most societies tricksters are represented as snakes and Lorkhan is famously known for being a trickster.

So the theory goes that for thousands of years this battle between Lorkhan and Akatosh continued until Talos came around, imprisoning and usurping the weakened Lorkhan in order to end the eternal battle between the two deities in favor of akatosh.

Now we come to another common theory of TES heroes, each one being a Shezarrine, what is a shezarrine exactly?

http://www.uesp.net/wiki/Lore:Shezarrine

Often associated with Lorkhan correct? So what if each TES hero is being guided by Lorkhan to in a way deactivate the towers? In Daggerfall a tower is deactivated by the Imperial Agent, in Morrowind by the Nerevarine but than we hit the Champion of Cyrodiil and another theory, that each TES hero is being guided by Talos. That leads to another idea, that both the imprisoned Lorkhan and the usurper that is Talos are guiding the characters but they are fighting against each other for dominance over the actions the characters take in the storylines with Talos seemingly always winning but Lorkhan actually winning in deactivating a tower. But why would Lorkhan deactivate the towers? Why would he unmake his own creation? What if the towers don't unmake mundus but just end the Kalpa which frees Lorkhan from his prison. Another idea is that the Nerevarines job wasn't to defeat Dagoth Ur but to free the heart of Lorkhan so Lorkhan can reclaim some of his former strength? Which Talos can't interrupt because he realizes that Dagoth Ur needs to be dealt with. This also leads me to another point.

The Oblivion Crisis. What we know of the Oblivion Crisis is that Mehrunes Dagon tried to conquer Tamriel, correct? What if that was nothing more than a lie? What if Mehrunes real goal was to retake Tamriel for Lorkhan or to destroy the towers, we know that Mehrunes once served Lorkhan as the leaper demon king before Alduin ate him in the previous Kalpa what if he is still loyal to Lorkhan and still served him. My next point will explain something that is left in mystery.

The void night.

http://www.uesp.net/wiki/Lore:Void_Nights

The Void Nights was when the two moons, often depicted as the rotting corpse of Lorkhan, was Lorkhan's attempt to reclaim his body on Mundus but ended up failing. This will also bring up another point I would like to make, the possibility that the Thalmor are nothing but unknowing pawns of Lorkhan and the leader of the Thalmor a possible Shezarrine. Think about it, if the theory I just stated is correct who would gain the most from Talos going away? His prisoner, Lorkhan so it brings to thought that Lorkhan is using the Thalmor to set himself free from the prison he is kept away in to reclaim his old position.

I hope you like the theory and I would be glad to hear any feedback or criticism on the subject, again the original theory was made up by FoolishOwl so they deserve credit for it too.

I still dont understand the jump from the void nights to the Thalmor being Talos' puppets.

And im still dont think the destruction of the towers is particularly helping lorkhan, and I dont think Talos would want to help any elves

The Thalmor may not care about the moons but I wasn't suggesting they do, what I was suggesting is that Lorkhan tried to reclaim his old body to regain his power to further break out of his but failed and that's why we have the void nights.