I read the Mutant Empire series as one book. I found it to be an enjoyable read and much less childish than I might have initially expected. The story is about Magneto, a powerful mutant taking actions to create a society for mutants and eventually expand to take over large portions of the planet. Of course, The X-Men intervene.
In the first book, Magneto and his crew attack a secret military base and take control of Sentinals, giant robots of immense power. With the Sentinals, Magneto and his group take over Manhatten.
At the same time, Cyclops finds out his father is to be executed on another planet.
The X-Men divide into two groups to attempt to tackle both missions.