The government is comparing mutants to weapons, trying to get them all to register, but the real villain of the movie is MAGNETO.
There is now a US general who used armed soldiers to seize a school building full of children and who has captured the X-Men's leader and is using his brain to wipe out the entire mutant race. The real villain is still MAGNETO.
There's been a "cure" discovered that deprives mutants of their mutation and has been weaponized. Also, Jean Grey, one of the X-Men's own, has come back from the dead as a terrible being of unfathomable power. Somehow, the real villain of the movie manages to be MAGNETO.
Sebastian Shaw has been torturing, abusing, and manipulating mutants for decades, and he and the Hellfire Club plan to start WWIII. The villain of the movie is MAGNETO.
The US government is sanctioning a program that will lead to a dark timeline in which mutants are hunted by robots and rounded up in concentration camps. The villain of this movie is not Bolivar Trask, who is building the Sentinels, or Mystique, whose actions inadvertently cause the timeline to come to pass, but MAGNETO.
Apocalypse is a big scary dude from ancient times who wants to see the whole world burn. But don't worry! Guess who's still a villain? MAGNETO.