The Elder Sea God isn't slumbering, like everyone thinks- it entombed itself with another Eldritch Horror, a genuinely evil one. The Sea God is the only thing keeping the really bad Elder Thing from getting out and destroying reality.
Of course, nobody believes this as the really bad Elder Thing happens to have just a little more influence on our reality. Over the past few millennia, it has warped minds in order to alter stories, records and public opinion of the Sea God. Now, nobody knows of its existence (except its cult) and the Sea God has taken its place in the public mind as the ultimate horror.
The Really Bad Elder Thing's cult has been working overtime lately. They found a way to get the Bad Thing out of prison without releasing the Sea God as well. All signs point to "wake up time!"
That is, until your BBEG (during the course of BBEG research) stumbled upon a Bad Thing cult hideout and a cache of records/journal/whatever detailing the Sea God and what it put itself under for- and how close they are to waking the Bad Thing up.
Of course, nobody believes the BBEG's story. Certainly not a bunch of loot happy adventurers.