I propose 3 different occupations. I will outline them from oldest to present.
The first occupation (ancient) was the constructor of the dungeon we enter through the portal. This civilization's technology is marked by the extensive use of a bronze like mettle, heavy armor, decorated weapons and furniture, lots of blue pottery, and spider iconography. This civ clearly had significant wealth. I suspect, but have little evidence, that they were somewhat more advanced than the civilizations that followed. We know the least about this civilization because we have few remaining written records. I would guess they existed at least 150-200 years before the game takes place. The only written records we do have speak of a council and discontent within the ranks of both the council and the guards. The skeletons we face come from this civilization. I can only guess that their motives had something to do with the power which lies beneath. There is a letter which speaks of a hero killing the gods, and this leading to inevitable demise at the hands of something "far worse".
The first 2 civilizations are linked by the portal. Who made this portal is unclear, but I would guess the first civ. If the second civ made it, why dig out such a underground staging point? Instead they must have built the staging point at the portal.
The second civilization is the one that built the dungeon before the portal. We know much more about them because their writings are still intact. This means they cant have existed that long ago, certainly not more than 200 years. The dialect used in there writing is said to be different, so is spelling. This suggests that at least 150 years have passed. They organised a huge industrial effort to build and outfit this dungeon with what appears to be industry to create a military expedition. They then opened/pass through the portal and explored the first civilization's remnants. They moved supplies, and even raw materials through the portal (see store rooms immediately after passing through). It is strange that we so no corpses from this civilization at all. That is, no corpses wearing there armor that were not clearly recent, and no fully equipped solders as corpses. It is possible that they did not suffer any significant losses in there expedition? This lack of corpses makes little sense to me. All the wooden equipment and furniture we see come from this civilization. Most of the weapons before the portal also come from this civilization (with some notable exceptions, i.e. the proctor). The architecture and outfitting of the dungeon shows clear class divisions in this civilization. We see prisoners chambers, barracks for solders, and large rooms with fancy decorations for whoever was running this effort. We also know from writing and from direct observation that they had organised heavy industry including pottery, glass blowing, mettle working, woodworking, etc. Nothing is said of their motives, but it is clear that they organised a military expedition through the portal and into Civ #1's ruins. It is also clear that they expected resistance as they build many barricades and defenses along the way. The technology of this civilization is marked by use of a silvery mettle, perhaps steel, wooden furniture and storage, little decoration, pragmatic design, and lots of written reports. There is some demonstrated interest in science shown by a book cataloging plants.
Both civ #1 and #2 had lights and torches that burn forever, showing some significant magical/technological competency (and possibly indicating that the existed at the same time/similar times).
The final occupiers of these lands are the current ones. There story has already been told in this thread so I will not repeat it. All the zombies we see come from the necromancy of the current occupants.
P.S. It is concevable that civ #1 and civ #2 existed concurrently, and civ 2 invaded civ 1?