Destabilization of the connection between dimensions causes portals to open periodically. The portals can have many effects and differing intensities. Some examples:
[ul][li]Ice: Perpetual cold, think ice lab but not confined to lab environment.[/li]
[li]Hallucinogenic: Nether environment messes with players mind causing them to hallucinate uncontrollably while in the zone.[/li]
[li]Darkness: Severely reduced vision capacity in this zone, not aided by night vision.[/li]
[li]Madness: Hallucinations + severe morale penalty + disorienting (character occasionally steps in wrong direction). Could be a more intense type of hallucinogenic zone. Minimap and map blacked out or otherwise incorrect somehow?[/li]
[li]Freaky weather: Acid rain, weird electrical storms, etc.[/li]
[li]Nether colony: Nether flora and fauna have established a foothold.[/li]
[li]Contaminated: Almost devoid of life. No grass, trees, or wildlife. Water may be nastier than normal. Nether creatures and zombies may remain, but in smaller numbers than would be expected. Non-sealed food is probably contaminated somehow. Prolonged exposure without protective gear causes sickness? Maybe litter the ground with corpses of all sorts?[/li][/ul]
An earthquake causes an ancient underground nether temple to be revealed that could have a nether portal inside.
A group of bandits move in and claim a small town or section of town as their own and start expanding their influence and raiding other towns and settlements.
Serious real weather events. A New England blizzard is nothing to be trifled with.