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Subterrain offers 4 different playing difficulties: Easy, Normal, Hardcore, and Nightmare. These modes change gameplay aspects such as Albert West's needs, damage to and from enemies, the accumulation rate of contamination, infection rates and how quickly the infected evolve, and where you can save.

In addition, a permadeath option can be selected, and is a separate setting from the actual difficulty. If permadeath is chosen, the new game file will be deleted if West dies, including any associated autosaves. The game files are not deleted if the death occurs during a boss fight.

Your placement on the in-game leaderboards are based, in part, on what difficulty you play on (permadeath is ignored). Playing on a higher difficulty does not place you in lower difficulty leaderboards. However, playing higher difficulties will reward achievements that require lower difficulties.

In addition to the differences below, the remote terminals in Nilson Engineering and Central Control require level 2 software to be installed on Hardcore and Nightmare; on Easy and Normal, they only require level 1 software.

Difficulty Easy Normal Hardcore Nightmare
Hunger/Thirst Needs 70% 80% 100% 120%
Enemy Health 100% 100% 130% 150%
Damage to Mobs 150% 100% 100% 100%
Damage Taken 60% 80% 100% 120%
Contamination Effect 60% 80% 100% 120%
Evolution/Infection Speed Slow Normal Fast Faster
Save From Pause? Yes Yes No No
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