Ahh...a challenge!
Bones
Earth Elemental
Ghouls
Magic Key
Kuo-toa
Holy Ground
Chairman Kaga: Watakushi no kioku ga tashika naraba...(If memory serves me right, it was the year of the Impossible Flood. The earth shook and the river flowed backwards as waters rose to cover the fields, and the best efforts of the villagers could not hold them back...)
Yomigaru Iron DM!
Act I: A River Runs Through It
The story begins (for the PCs at least) immediately after the flood, in the village of Canphael along the banks of the River Wesset. As they approach the town for their own reasons, they hear tales of the shuddering earth and the river's mysterious backwards flow.
Upon arriving in the village, they see the people trying to rebuild, each doing what they can, from salvaging what they can of houses to replanting crops in a desperate attempt to salvage what is left of the season. The druid Pendar is chief among the rebuilding efforts: as the party arrives he has summoned a massive earth elemental to help clear away the trees and the like that were swept upstream with the waters.
As the horrified villagers look on, the elemental goes berserk, and it is up to the players to try to stop it. During the fight, it begins to speak, shouting out curses against "those who have disturbed my bones". Clearly something is unusual...
If the elemental is destroyed, a strange, inhuman skeleton will be found inside it - it seems it was swept upstream with the other debris. Clutched in its skeletal hands is a strange key made of coral.
On the other hand, the characters may be able to parley with the elemental - if they promise to restore the bones to their resting place, it will recede. "Take them to the sea..." he asks. "The key must remain with them."
Pendar is convinced that the earthquake and flood were not natural, and he begs the party to take on the task of investigating - and laying the bones to rest.
Act II: Down by the River
A journey downriver reveals much the same situation as in Canphael - villages have been wrecked and flooded, and nobody knows why. What should be a few days of travel takes weeks, passing through the destroyed plains until finally reaching the sea. Along the way, the PCs hear tales of ghoul sightings, and even encounter the creatures themselves. Strangely, the ghouls seem to be searching for something other than food...
At the mouth of the river, the port town of Grottmere has been completely shattered and abandoned - only one hermit remains behind. He does not know what caused the flood, but he can identify the skeleton as being that of one of the fish-men that used to live in the ocean. The kuo-toa were wiped out centuries ago - legend has it that they meddled in things better left unmeddled-with.
It seems that the answer lies in the ocean itself...but first, more ghouls. This group is armed, and has some class levels, and the leader is carrying a strange magical device - a compass that points not to north, but to the coral key.
Act III: Holy Ground, Drylander
The kuo-toa city, when the characters finally arrive, was obviously the epicenter of the earthquake. It is largely destroyed, having been scattered by the quake and the flood waters. Ghouls roam the streets, forcing the party to sneak as well as they can. There is one area of the city where they seem unable to go - the crumbled remains of what looks to have been a cathedral. Many of the ghouls encountered will have levels - wizards, clerics, and monks are all possible. When the party is noticed, a veritable army of ghouls will chase them - the cathedral is the only safe haven.
Inside the cathedral they find metal tablets inscribed with the history of the fall of the kuo-toans: unwise experiments with extraplanar energies. It seems that the kuo-toans tapped into the negative material plane and opened a rift, draining their life energy and turning them into undead. Only the intervention of a great priest was able to save them by sealing the rift and locking it with a magical key - the very key the characters have in their possession. This act cost him his life, and the few remaining kuo-toa interred him in the spire of the cathedral as the key's guardian.
When the party reinters the bones, the spirit of the kuo-toan cleric appears again to them. It tells them that the ghoulish army outside is led by a powerful undead priest, who wants to get the key and use it to open the gate to the Negative plane again. The earthquake was caused by the priest, who hoped to topple the spire of the cathedral so that his minions could get to the key...
Now all they need to do is get past an army of ghouls, assassinate their high-level ghoul cleric commander, and escape. Simple...right?