The Augmentation Room is a room for William Stryker to graft the metal adamantium onto mutants. It is located in Alkali Lake. It was initially destroyed after Cyclops destroyed the dam in his battle against Jean Grey, flooding the whole lake. However, after Wolverine manages to alter time, he inadvertently prevents Stryker's base's destruction.
Wolverine was placed into the water tank and had his entire skeletal structure grafted with adamantium.
Wolverine tries to find answers and ends up battling Lady Deathstrike. He impales her with an adamantium injection which solidifies her from the inside out, preserving her unconscious form inside the water tank, presumably killing her.