Setting off on his own, Stryker developed a program to use mutants, particularly brainwashed ones, to carry out his plans. His main method of control was using fluids secreted by his son's brain. Stryker's organisation was headquartered at the Alkali Lake dam in an underground facility, though it also maintained offices in a federal building somewhere in the Washington DC area. Stryker's group has ties to Muir Island, Project Wideawake and keeps a kind of register of mutants. The organisation was also responsible for designing the plastic prison where Magneto is imprisoned. Stryker is also connected to Wolverine's past and his augmentation with adamantium. Stryker's organisation also had a number of other mutants including Sabretooth in its custody, several of whom were freed by Logan. Stryker was also responsible for augmenting Yuriko Oyama with adamantium, and giving her the same healing factor Logan possesses. Stryker plots to use a brainwashed Nightcrawler to attack the White House and enable him to raid Xavier's school and capture Xavier and components from Cerebro to attack mutants and kill them all.
Following Stryker's defeat at the hands of the X-Men and the Brotherhood, he was left chained to a helicopter as the dam burst. He presumably drowned in the ensuing flood.
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