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Weapon X is a codename for a secret US government project intended to deliberately induce superpowers for military purposes, turning willing and unwilling beings into living weapons.
The project often captures mutants and experiments on them to enhance their superpowers and also mutates baseline humans.
The successive projects had Roman numerals, so Weapon X and Weapon XI were the tenth and eleventh such projects of the Weapon X program.
After capturing Moira MacTaggert, Beast, Mystique and Quicksilver, William Stryker takes them to Alkali Lake. Scott Summers, Jean Grey and Kurt Wagner discover Logan (dubbed Weapon X), and Jean frees him with her powers as Logan/Weapon X attacks the guards. Meanwhile, Stryker escapes via helicopter while Logan tries to attack Scott and Kurt, although Jean calms him down and restores a part of his memory, just enough to give him sanity and allows him to escape into the wilderness.