The Mutant Control Agency was a private organization based in Washington, D.C. and was occasionally sponsored by the government. The organization was created for the purpose of registering mutants of a voluntary basis. However, these mutant files were intended to be used to track down and capture mutants. The agency was apparently funded by Henry Gyrich, who also paid Bolivar Trask to produce the Sentinel robots.
The X-Men learned that the Mutant Control Agency had been supplying details of their registered mutants to the Sentinels and decided to break into the Agency's headquarters to destroy the files. During this raid, Morph was apparently killed and Beast was arrested.
Following this raid, the President of the United States (who publicly claimed that the Agency's headquarters were those of the "Federal Security Agency") demanded that Gyrich shut down his Mutant Registration Program. Gyrich decided instead to move the Sentinel program overseas (to Genosha), in case he was ordered to shut that down as well.
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