I forsee two possible settings to this disaster endgame mode: "Complete Disasters" and "Mild Disasters." In "Complete Disasters," every disaster will ultimately destroy the planet entirely if nobody reverses it before it runs its course. In "Mild Disasters," the disasters will only do serious damage to the planet, but the game will go on, and disaster types that would end the world are disabled.
You could also have a "realistic disasters" mode and a "fantastic disasters" mode.
Mechanical possibilities for various endgame disasters:
1. Ice Age. On a certain turn, the ice age triggers. Every turn, X water or ice hexes (determined by map size) along the ice caps turn into ice cap terrain (the non-traversable except to submarines kind), X tundra hexes turn into ice hexes, the same number of grasslands become tundra (always along the northern edge), X plains become grasslands, X deserts becomes plains, and X jungles become forests. Any city or improvement which ends up under an "ice cap" is destroyed; units that end up on one start taking damage every turn. In "Complete Disaster" mode, this happens until every tile is an ice cap. In Mild mode the ice caps would only cover ~2/3rds of the Earth's surface.
2. Global Warming. The opposite of Ice Age. Could be set to Anthropogenic (Mild Disaster) mode, Solar Warming (Mild Disaster) mode, or Solar Flare-Up (Complete Disaster) mode. Tiles progress in the opposite direction of Ice Age above, except a new "dust" tile type would be what destroys cities and improvements and damage units. Additionally, jungles would still become forests, and forests would sometimes disappear. I imagine it stopping with a little less than 1/2 of the planet's surface being a dust tile.
In Anthropogenic mode, you could save the planet by going green and convincing other nations to do likewise. In Solar mode, you couldn't do anything to save it, but it would peak at ~1/2 as above. In Flare-Up mode, you couldn't save it and it would eventually destroy everything, necessitating escape of the planet on a spacecraft.
3. Infection. In mild disaster mode, this would simply start causing massive unhealthiness that would reach a certain peak, and could be reversed by devoting research points to finding a cure. In complete disaster mode, there would be no peak to the unhealthiness, and any city still in negative food at 1 pop would die out and become "unowned." Any player could then settle the city and take control of all of the buildings in it. In fantastic disasters mode, this would be more like "zombie apocalypse" mode, with a random city on each continent plus a few extra falling to the infection that then begins losing population quickly and spawning waves of "infected" units. Any military unit in direct combat with an infected unit would become an infected unit in 1-5 rounds (and are therefore only useful as a delay), unless and until enough research points are invested in finding a cure, at which point your units are safe if you can exterminate any remaining infected threat. Might be fun to be faced with the decision to share the cure you've researched or let your enemies get run down trying to research their own. U.N. Victory is still enabled, but just gives you control of all cities and units to fight the zombies with until they're defeated. Space Race victory still functions normally. All other victory modes don't kick in until after the zombies are dead.
4. Alien invasion. Fantastic disaster mode only. All victory modes disabled, other than U.N. which functions as in zombie mode. The only way to end the invasion is to research and produce a doomsday weapon powerful enough to shoot down ships while they're still in space or possibly an inter-dimensional weapon. Normal victory modes become re-enabled after this is built.
5. Meteor/Comet collision. How much early warning you get is based on your tech level; optics warns you only a few turns in advance, and any "detection" tech such as radio, satellites, computers, and the like give you more warning. The collision would destroy a large area around the impact site and create "wasteland" tiles that function as dust or ice cap tiles above, except without the damage over time. The severity of the climate change after impact would depend on whether you had set the game to mild or complete disasters, but would probably follow similar guidelines as the ice age disaster type. This exact set of mechanics could also be used for a "nuclear disaster" end-game mode.
Any other ideas for this? This would make an epic mod.