Nick Fury is one of history’s best spies, but there’s only so much he can to with subterfuge and firearms if Earth is threatened by unusual forces.
After seeing Carol use her amazing abilities to defeat the Skrulls and any other enemies that might pop up in the movie, Fury will start looking for individuals who fit this criteria, though it will be many years before he successfully implements this “Phase 1” project.
We don’t know the specific details about Captain Marvel’s plot yet, but if Nick Fury does play a hand in helping Carol battle the Skrulls (which might result in him losing his eye if we consider his trust comment from The Winter Soldier with the fact that Skrulls can shape shift), then his experience in this ’90s alien brawl fest will plant the seeds for what will eventually become the Avengers Initiative.