The Federal Bureau of Prisons (BOP) is a subdivision of the U.S. Department of Justice, responsible for the administration of the federal prison system.
The President's administration, in partnership with Worthington Labs, developed the "mutant cure". Publicly, Worthington Labs promoted the cure as a voluntary way of dealing with mutation. Privately, the cure was already being weaponized, initially by the Federal Bureau of Prisons, as a contingency plan to deal with threatening mutants once they were in custody.
After her botched FBI interrogation, Mystique is later put under the jurisdiction of the BOP, and is placed in a prison convoy for transfer to a more secure location. The convoy was also carrying James Madrox and Cain Marko.
Following the Brotherhood's attack on the prison convoy, they discover and make public the fact that Worthington's cure was being weaponized.