How about this:
The temple above once housed an ancient cult dedicated to some creepy super evil being, like Far Realm kind of creepy evil. As the cult delved deeper into the temple, they dug into the caves. As they explored the caves, they found an ancient crypt/shrine (area 11) dedicated to the creepy evil super being, which predated the temple. Inside the crypt/shrine was a sacred pool that acts as a portal to the Far Realm where said creepy super evil resides.
Before the cult could access the portal, they were attacked and enslaved by an Aboleth that wandered into area 10 from deep below where aquatic tunnels connect to Underdark waters. The aboleth was able to learn of the portal in area 11 and believed that it could utilize its new thralls to summon some Aboleth elder evil from the portal. More cultists descended to the caves to find their buddies, but they too were enslaved. Eventually the cult above fled, avoided the caves, or were wiped out by adventurers / rival cult, whatever. Time passed, but the Aboleth could never get the portal to work as his cultist thralls lacked the power. The cultists, twisted and evolved into Skum continued to slave away for their master.
One day, a tribe of bat-humanoids (or other sentient bat-like creatures), led by their spiritual leader (cleric or druid or something) found the entrance to the caves (area 1) and sought to make their home in the caves. Eventually the Aboleth found these invaders and learned that their spiritual leader was powerful enough to unlock the portal and the aboleth sought to enslave him. A war began between the Aboleth and its Skum and the bat-humanoids.
In one final battle, the bat-humanoids managed to defeat the aboleth, but at great cost to themselves. The bat-humanoids fled to their section of the caves and the Skum were freed.
The Skum have banded together under one head Skum who has revitalized the worship of their creepy far realm evil thing and their cult lives on deep in the caves - they still seek to summon their thing. The Skum cult-leader is growing in power and will soon be able to summon forth a great evil. The bat-humanoids still seek to claim the caves for themselves and continue to skirmish with the Skum, fearing that the aboleth still lives as his thralls remain.
The PCs find themselves trapped between this long-standing battle and can choose sides, play them against eachother or wipe them both out.
We can really get the history of the conflict across with some subtle hints: the skum still wear the tattered remains of their robes that still have unholy symbols on them (gives the PCs a chance to learn about their religion), the old temple chambers can still hold unholy items or more information about the religion, on the rocks of area 10 could be the bones of the aboleth as the Skum feasted on their former tyrant in order to survive, etc.
Area 10 could now hold some new guardian creature, perhaps some aquatic terror that the SKum managed to bring up from the underdark tunnels...
Just a quick crack at a story as I procrastinate here at work. Thoughts?
Or, perhaps the Aboleth has just found a soul strong enough, perhaps from somewhere else in the cave (Grimlock explorers from the underdark, other adventurers, etc.) and his Skum cultists are preparing to sacrifice him in area 11 which will bring forth the evil smack down. The PCs must learn whats going on and stop the sacrifice? Or maybe the sacrifice is done and the evil is awakening through the portal and is weak enough for the PCs to take it down?
