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An idea for a potential mod for 1.9:

A fungal contamination mode, where the mushroom biomes just spread until they cover everything. You can keep them out with a wall which goes 8 blocks above and 8 blocks below ground and to de-contaminate you've got to immerse yourself fully in water when going into a clean biome or the spores will come with you and contaminate your home.

Monsters would be able to spawn during the day in contaminated areas. If it is impossible to achieve this, their spawn rate would be doubled. You also slowly lose health when in these biomes and the mycelium cannot be farmed.
Alternatively, think of your own threat.

It would also have to spread slowly enough that not dealing with it within your first couple of nights does not scupper the game completely because that time's usually needed for the basics of survival but fast enough that it actually poses a threat which has to be dealt with eventually.

You'd have to be extra careful of spiders climbing over the walls in case they brought spores with them.