Why Pandaria? What were the Mogu sent to protect? Or destroy? -Wrathion
With all we've been told from Ra-Den and Wrathion in 5.2, mentioning of a 'yawning chasm' and something evil beneath Pandaria. Now, we know whenever there's talks of something buried beneath Azeroth, it is almost always connected to the Old Gods. And guess what, theres a dead Old God somewhere in Pandaria. So, it is obvious that whatever is beneath Pandaria is related to Y'Shaarj. But Y'Shaarj is dead. Very dead. So how can he still pose a problem to the people of Pandaria?
We know that the Titans decided against killing Old Gods, because apparently their death will bring about Azeroths demise. In MoP, we learn one such consequence that comes from killing an Old God; The Sha, the essence of Y'Shaarj that still lingers on Pandaria, and can manifest itself when their is strong negative emotion, exactly the feelings the Old Gods inspire. The Sha have a very, disjointed historg. In 'The Swarm, the Stone, and the Storm', we learn the Sha haunted the land almost immediately after Y'Shaarj's death, but what about during the Mogu empire? Why does it seem that they were completely unaffected by the Sha, despite the Mogu being riddled with emotions like Anger and Hate.
But a better question. What is the of Nalak'Sha, and what was Ra-Den doing there when Lei Shen 'found' him?
We know that after the Titans left the Mogu, they were afflicted by the Curse of Flesh, and Ra (Den), their master, fell silent. It was during this time that the Mogu broke up into seperate clans, and fought against eachother and other Pandaria races. Legend says, that after he began uniting the clans, Lei Shen marched solo into Mogu'Shan vaults, and in a secret chamber, found Ra, guarding a mysterious Engine, now called the Engine of Nalak'Sha. To this day, no one knows the point of the engine, or why Elegon, its defense mechanism, a cloud serpent? But, despite all the deaths us players experience on this boss, very few people have wondered,
Why is there such a long tunnel beneath the engine?
SPECULATION
Ive been thinking of how this can all come together, and then it hit me. Ra-Den remained on Pandaria to find a way to remove the Old God presence, the Mogu remained incase Y'Shaarj somehow returns.
After the CoF afflicted the titanic races, and the Titans themselves left, Ra-Den went to experiment on the Sha and Y'Shaarj, in an attempt to remove the Old God presence from Azeroth, which he believed would result in its doom, without having to deal with something like the Sha. These experiments were done ontop of Y'Shaarj's corpse, in what is today called the Engine of Nalak'Sha, built inside the Titan complex there.
When Lei Shen found Ra-Den, he didn't beat him, he convinced him. Ra-Den believed the way to deal with the Old Gods and the Sha would be absoulte removal of all races afflicted by the Old Gods, all races he deemed corruped. Lei Shen told him otherwise; Give him the power of the Gods, and he will build an empire under one banner, that be so orderly thered be no chance the Sha could be a problem. And right after recieving this power, Lei Shen proceeded to betray and imprison Ra-Den, as punishment for him deserting the Mogu.
Lei Shen had his best spellcaster, the Korune, toy with the engne, in hopes of finding a way to make the Sha a weapon. After finding Nalak, his favoured pet, he had Elegon, the computerized defense mech installed by the Titans, made into an image of him. However, the Mogu would NEVER attempt to manipulate the power of Y'Shaarj himself, that goes against everything they were built for.
Fast forward, we have Ra-Den, after being freed, immediately proclaim he is going to cleanse this doomed world. After his defeat, he remarks about something evil either inside or beneath us. Wrathion later mentions that an evil exist beneath Pandaria.
After the Mogu are decimated in 5.2, whatever forces remain are lost without leadership. At the same time, Garrosh is eventually gling to hear talks of a rebellion, hes going to grow desperate (even moreso) in who he recruits.
So what i see happening. Some Mogu pledge allegiance to Garrosh, seeing him as there best chance at glory. In return, they tell him information about an incredibly powerful and ancient being beneath Pandaria, who would be unable to stop Garrosh from draining its power. So Garrosh attempts to harness the power of Y'Shaarj. He gets some of his best spellcaster to transport the remains of Y'Shaarj himself into RFC. Because we defeated the Sha, Garrosh will have a much easier time controlling this power and weaponizing it. He uses the Old Gods energy to create Twilight Fel Orcs.
For the final fight, Garrosh is incredibly powerful after draining the energy of the Sha and Y'Shaarj into himself. However as the fight goes on, and he becomes more desperate, Garrosh suddenly gets possessed by the final Sha, the hidden one that brought a out the end of the Mogu empire, and that has affected every race on Pandaria without any of them knowin. The Sha of Pride. Garrosh passes out, and the 7 Sha are released, and the final boss becomes a semi-ressurected version of Y'Shaarj, the God of War.
Tl;Dr Ra-Den was researching the Engine of Nalak'Sha, which has Y'Shaarj buried beneath. He 'gave' Lei Shen the power of the titans so he can build an orderly empire. Mogu stragglers post 5.2 will join Garrosh and tell him about the power of Y'Shaarj. Garrosh brings his corpse to RFC, experiments with it, and gets possessed by the Sha of Pride, which causes all Sha to form into a weakened version of Y'Shaarj.