After the Weapons Plus Project was shut down, The Facility was created as a branched-off organization with similar goals of creating genetically altered weapons and soldiers.
Under the direction of Adam Harkins this organization created Kimura and Native; successfully cloned Wolverine; several mutant hunting Predator X monsters; and numerous other genetically engineered weapons.
Later, Kimura assaulted X-23 and Mercury, not to capture Wolverine's clone but to create new Predator X using Mercury's powers of liquid metallic body.
Adam Harkins utilized a red lab in Canada to use the stolen wings from Angel to create the Choir, an army of winged warriors, for Matthew Risman's Purifiers.
Returning from the future, X-23 was kidnapped by soldiers of the H.A.M.M.E.R. who were revealed to be Facility agents, in the exception of Alisanda Morales. When Kimura was torturing X, Morales helped her to escape.
X-23 uses on herself the chemical principle created to made her a savage killer, and killed many agents of the Facility before being extracted by X-Force. Kimura killed Harkins because he annoyed her, and blame X-23.