He is supposed to be sort of the Pandaria version of Thorim. The difference is that while Thorim existed with many other keepers at Ulduar, due to the large threat posed by Yogg-Saron should he have escaped Ulduar, it seems Ra-Den was left to guard the Engine of Nalak'sha all by himself.
This became a problem when the Mogu, former servants of the Titans that were transformed by the curse of flesh, turned twisted over time and one of them, Lei Shen, entered the vaults and did battle with Ra-Den, somehow winning and ripping out the titan keeper's heart, which is what has given the Thunder King his power.
Since then, he was taken to Thunder Isle and locked inside the Thunder King's fortress, his "flesh" taken and used in experiments in fleshshaping. Likely when the Thunder King was killed during the rebellion, the mogu abandoned the island and Ra-Den was kept locked deep and alone below the fortress, possibly going mad.