Grand Admiral Thrawn is ordered by Emperor Palpatine to work with Lord Darth Vader to undercover a secret Invasion by an unknown party connected to former Shield Director Nick Fury who was declared dead during the events of Order 66. Thrawn and Vader discover a rogue group of Skrulls led by Gravik. They're behind the Invasion and they seek to use a mysterious weapon to cover the Earth in irradiation so only their species can live while every other human and non human species dies. Nick Fury and his Skrull ally Talos seek to protect the remaining peaceful Skrulls. While Thrawn seeks to find out the group that supplied the rogue Skrulls with weapons for reasons other than protecting the Empire. Thrawn's secretive motivations cause tension between himself and Vader which exacerbates the tension the two Imperial leaders have with Fury and Talos. The four must put aside their differences and use Thrawn's memory of an old mission he went on with Anakin Skywalker and Iron Man to expose the rogue Skrulls employer and foil their plans..