Shortly after the Cuban Missile Crisis, Magneto and Mystique defected from Division X. With the remaining members of the Hellfire Club, they almost immediately became recognized by the FBI as terrorists. The Brotherhood was pursued relentlessly by Project WideAwake, whose members killed Azazel and Tempest before Mystique assassinated John F. Kennedy. Following this, Magneto surrendered himself and was given two life sentences.
However, eventually Magneto escaped and reformed his Brotherhood, with Mystique being the only returning member. Instead he was joined by Toad and Sabretooth. Both of the two new members were killed at the Battle of the Statue of Liberty. After several new recruits, the Brotherhood was eventually finally disbanded after the Battle of Alcatraz.
The Brotherhood of Mutants was a pro evolution group, believing that mutants were bound to inherit the earth as eventually all humans would gain powers. With this belief in mind, they fought to establish a survival of the fittest regime against the humans. While not anti-human, the Brotherhood deeply valued ties between mutants and would rather kill a human than even a mutant from the X-Men.