The horror of the Black Death was severalfold:
1) No one knew - for certain - how it spread. Someone who looked healthy could actually be infected - and spreading it to others. It seemed to strike suddenly and seemingly randomly - amongst the poor, the wealthy, etc.
This will be the hardest part to recreate, considering divinations, etc. Perhaps a Far Realms entity briefly was upon the prime due to some horrific Alienist ritual in an obscure location. The disease receives SR vs magic - both divinatory and curative, and those that become infected may seem healthy for 5d6 days (ave: 17.5 days) before showing symptoms - which rapidly and horrifically lead to death (perhaps gaining some minor aberrant traits for the few days its takes to die - making catching it more horrific). After death have them rise as undead (remember to apply the SR to attempts to control or turn) - to further horrify the populace.
2) It had several different versions dependent upon how it was contracted - which some viewed as different diseases. If contracted by flea bite it developed normally - and slowly: swellings that blackened (thus the name), etc. If it was breathed in (breathing the mist from a cough, etc by accident) it developed severe pneumonia style symptoms that - if I recall correctly, eventually had the person spitting out either blood or a blackish bile from their filling lungs. This tended to kill a person in days rather than weeks (as with the flea bitten way). The final - and swiftest and most certainly leathal way - was direct blood contact. An open wound infected by shed blood / bile from an infected resulted in an infection that arose within no more than a day and slayed an otherwise healthy person within hours - always.
This ties in well with the prior point (1) and its aberrant traits concept. Perhaps the disease is actually attempting to transform the individual into a type of far realms creature, but most do not survive even the initial minor stages of transformation - and the transformations for each creature affected differ markedly. If the disease occationally affects non-humanoids (animals, magical animals, monstrous humanoids, or even plants) it makes the disease all the more confusing and disturbing.
3) Nearly everyone who sickened died, regardless.
Treat it as a normal disease with a high Fort DC. Note that with the SR this DC does not have to be all that high. Even high level characters, without the aid of magic, could readily die of an infection whose DC was 20 - 30. Especially if magical means of increasing Fort saves do not apply due to the Far Realms style malady's resistance to magic.
4) Its spread brought about famine (due to depopulation of farming villages).
This works well without much adjustment. The idea of using undead to deal with this issue is nice and leads directly into later adventure hooks, but consider that if those that die of the malady become undead that are difficult to control then it becomes difficult to distinguish between the undead that are supposed to be there (under control) and one that wanders in from the nearby forest when the overseer was not watching. Just a few deaths due to this - especially if the undead responsible had few or no notable physical alterations from the malady - and many will discourage the use of undead due to the potential for the spread of the disease (as these risen zombies that died of it will certainly be contageous - and may even have ways to transfer it to other undead).
Regardless, famine will occur, leading to increased depopulation. And if the malady raises infected zombies that can pass on the infection to other zombies met - or to recent corpses - then the infection may spread even more spectacularly.
5) Other diseases also saw comebacks at this time, increasing confusion as to what was or was not the dread Black Death. The panic over the Black Death often lead to those regions where it hit being abandoned or set afire (preferably from afar, which leads itself to poor likelihood of completing the job). These regions typically became areas where other diseases could readily grow and spread to looters - who passed them on to others they met.
Thievery should be punished more strickly for a time, due to the danger looting resulted in for any community that was battling the plague. Anyone that enters a region that has more or less been almost completely depopulated due to the plague should have to roll verse having to make a fort save vs contracting a disease (the Far Realms Malady being first likely, but others also being possible - say 60% for the main disease, and 5 - 10% for each of the remaining potential diseases.
6) War was an almost constant possibility. Lands may come to the edge of war over whether one was in some manner responsible for the spread of the plague into the other land. But lower populations and decreased food supplies would have discouraged war (as the supplies to maintain it or hold lands after winning it - presuming it could be won - were lacking). This antagonism, however, could persist until after the wave of the plague had mostly passed - allowing for flare ups after its passing.
After the malady passes almost every land with neighbors will have very high strung relationships - a cold war that could result in war upon the slightest provocation. I imagine that after the plague passes, after the famine that resulted from the lack of man power begins to let up, war will become the next main anguish for those alive, each land paying back a hundred slights and suspitions built up over the years of famine and plague.
After this things should calm down a bit. When the dwarves and elves return (perhaps not unaffected by the disease, as these wandering contageous zombies may have accidentally found their way into an elven forest, a forgotten entrance to a dwarven mine, into a river that supplies water elsewhere, etc) the map should look notably different - borders altered, alliances altered, etc.
Undead should be feared more than normal, as for a long time any that were met may have potentially been infected. Thievery should be punished more severely for a time. The lands should exist in an uneasy truce. After years of war they are finally at peace, but it is a recent thing, and no land has fully demobilized its armies - just in case. It will take more than a minor thing to set off a local war, but it won't take a particularly major issue either.
The disease? Perhaps:
The FRM [Far Realms Malady] is a Contact disease requiring a Fortitude save of DC 25 to resist infection. No magic items or spells may enhance this save. Once infected the N/PC is contageous and may infect others, but they do not take initial damage for 5d6 days. All attempts to detect or cure the infection by any means suffer against SR equal to 4d6 + half the HD of the infected.
After they make their first save the disease speeds up its effects. The first Fortitude save deals 2d3 Con and 1d4 to Int, Wis, and Cha. One point of the Con damage is instead drain. Every following Fortitude save is made 4d6 hours after the prior, such that some may die swiftly while others linger for days. Recovery requires three successive saves. Any mutations gained before recovery are permanent, although ability damage may recover as normal.
Each failure results in a minor transformation - the skin may dry and wrinkle - or become bloated, or change colors, or gain (or lose) hair, or grow scales, etc. Or perhaps the eyes will sink or protrude, or change color or pupil shape. Or perhaps horns or tusks will grow. Or perhaps the fingers will wither into bony claws - or fall off, or grow additional digits or knuckles.
Each failure should result in a minor but readily noticeable 'drift' or 'mutation'. It is far realms, so it should be different each time for each person, but local versions of the disease may have common patterns - perhaps most (not all) gain a skin alteration (dry, brittle, perhaps always some shade of red or green), etc. The Geomancer drifts, the Ravenloft power check penalties, the Taint penalties, and the Genasi, Tiefling, and Aasimar physical / unusual traits (hair moving as if in a wind, smell of brimstone, faint glow from skin, etc) are excellent sources of inspiration for these.
After death the deceased rises as a contageous zombie 4d6 hours. They receive their HD as a bonus against Turning and retain their SR - which now affects all detection divination (such as Detect Undead, Locate Creature, etc) and specifically Undead harming magic and items used against them. This makes them more dangerous than typical zombies (as they are harder to turn, dangerous in melee (due to contageous nature), and resistant to most spells used to combat undead.
Every year after the plague first strikes, decrease the disease's SR by 1 due to the disease weakening, the magic used against it strengthening (as the deities get an idea of what their followers are dealing with, etc), and resistance to the disease slowly building. Each -6 to the SR results in the removal of a d6 when determining the SR of the N/PC's infection (to 3d6 + half HD, then later to 2d6 + half HD, etc, eventually leading to SR equal to half infected's HD). A year after the 4d6 is removed (25th year after the disease first struck) magic items and spells can once again affect the save, granting a sudden surge in detections and cures that mostly removes it.
Like the Black Death it will certainly arise again from time to time. Perhaps every 50 years after the infection's SR is mostly negated results in the regaining of 1d6. So after 200 years it would be just as virulent as before. Or, to better show the slow gaining of resistance to it, state that each time it regains its strength it loses 1d6. So after 150 years it is mostly restored (SR equal to 3d6 + half HD). Then 25 years later it is again faded, and 100 years later it is restored in potency (to 2d6 + half HD).
After this it requires 100 years to regain full potency (1d6 + half HD as SR), no longer fading but no longer blocking the effects of magic items / spells against aiding in overcoming the disease's SR. It is still potent, but now - after almost 500 years, its SR is barely an issue. Perhaps this is why most diseases in D&D do not have SR - they lost it millennia ago, and this disease is the first major one to arise with SR in all that time.
- - - - -
In the current - post plague - era undead are viewed with more horror. The Major Churches likely did receive some trouble from the plague (loss of confidence of the faithful, resulting in the rise of numerous minor cults and rival minor churches, etc). The Churches most antagonistic to Undead are likely to have the largest followings - not out of confidence in their ability to cure, but instead in the belief that they can destroy the undead that carry the plague.
Any sign of illness is viewed with mild but certain fear, as are undead. The church is again held in regard, but the certainty of that regard has been terribly shaken. The populace depends upon the church in many respects, but they no longer view the church as a surety of safety, protection, or aid.
The state has perhaps become more secular as a result, but it is also less firm in its control, for it lacked manpower for quite some time, and its wars after the plague / famine years further eroded its manpower, its control over the populace (more than one noble was overthrown by their own men to prevent a problem from esculating into a war - or to deal with practices that the populace felt were not sufficient or even dangerous to their welfare). The world exists in a delicate state. When city-states begin to rise, the nobles that survived the troubled times will be slow to exert notable force to control them (as such may have a negative impact against them), which will allow some of the city states to settle and eventually raise their own troops (eventually regularly paid mercenaries that move in, eventually becoming town guards, etc).
Trade will open the lands to new resources, new ideas, and new methods. The churches - if seeking to control or limit it - will find they either lack the influence they once had or that they are competing against so many new ones (that arose during the plague / famine / war years) that they will be mostly inaffective for decades. The secular lords will find that many of the city states neither need or want his advice or leadership - and have the troops to back up their wishes. Dwarves and Elves will be welcome with caution, for the plague / etc years would have built up susption toward all non-local peoples (as they might be plague carriers, out to steal food, spies from nearby contentious lords, etc).
But they will find the new resoures / methods more alluring than their fears - especially when most turn up groundless. The suspitions will remain, however, for quite some time, just on principle and tradition. So we have several small states developing that are not controlled by feudal lords, church, etc and have both new methods that the prior may want and the troop so maintain their independence and enforce their contracts, etc.
An interesting setting, I think.
Anyway, how does my version of your plague sound?
