"Secret Invasion" centers around Nick Fury confronting manipulated Skrull refugees threatening humanity

Nick Fury made promises years ago to help find a new home for Skrulls seeking refuge on Earth.
A radical Skrull leader named Gravik is taking advantage of Fury's unfulfilled promises to fuel anger towards humanity.
Gravik has developed a way to create "Super Skrulls" with the abilities of creatures like Groot to become a threat to the Avengers.
The show addresses the lack of Avengers involvement by suggesting Skrulls may have replaced them and addresses a lingering plot hole.
The deaths of Maria Hill and Everett Ross raise the stakes and leave Fury relying on allies like James Rhodes to help stop the Skrulls.