Like most Claremont X-stories, there are multiple simultaneous stories in these issues. The main one has Callisto tracking down Sugarman, who killed the Magistrates, and seemingly killing Sugarman.
A major subplot has Magneto and Xavier trying to restore Scarlet Witch from her coma (which followed the Avengers: Disassembled story). Magneto is so focused on saving his daughter that he hides other events from Xavier so that the Professor will keep trying to reach her mind.
Another: The Hellfire Club is looking to take Genosha–so says the new (and newly dressed) White Queen: Courtney Ross (aka Opal Luna Saturnyne).
She takes action to set up an outpost in nearby Zanzibar with Viper and the Weaponeers as their agent. The Excalibur team help defend it, but it turns out Zanzibar has its own hero as well: Askari.
This series is getting increasingly complicated, but it will also end soon. It’s hard to get too invested.