So there was this government plan called The Magneto Protocols that was designed to take out mutants who were deemed a threat, and Project Polaris was part of it. She and Random track down the source of the Project to cancel the contract out on Polaris, and fight other supers in government employ (Crimson Commando, Avalanche. In the end, we learn the government plot is actually the work of Malice of the Marauders
The government plot aspect of this is pretty “standard” X-Men stuff–it’s really about giving some background to Random, who, I’m guessing, is about to become a more central castmember.