Mutations are passive boosts you can unlock between levels. Different mutations give you different boosts, and you can have a maximum of three in effect at a time depending on how many areas you’ve cleared in your run. To unlock a new mutation, you must find its blueprint and then give the blueprint to the Collector. In addition, you’ll need to spend Cells to unlock the mutation.
New abilities are granted through runes. These are permanent upgrades that let you access new areas.
Blueprints are highly important. Some blueprints unlock new mutations, for a variety of passive effects, while other blueprints unlock new weapons, shields, secondary skills the player can equip for combat (two being equipped at a time), traps, turrets, grenades, and powers.