Matt Fraction established in The Order that the mayor of San Francisco has been looking for local superheroes, ever since the fifty-state initiative decided to headquarter the California team in LA.
Post-"Messiah Complex," the X-Men broke up for a while, and Cyclops and Emma wound up helping with a mutant problem in San Francisco. The mayor got in touch with them afterwards and offered them sponsorship, and thus the X-Men became the official superhero team/mutant liasons of the city of San Francisco.