After a mission led by Hawkeye and Mockingbird against Hydra ended with the secret revelation of Madame Viper being a Skrull, which was kept only to Nick Fury by Mockingbird, he decided to create a secret group of his allies in order to observe and try to find any other Skrull infiltrator hiding among people on Earth.
They contacted Tony Stark and alerted him about this situation. Days later, when a massive Skrull Invasion showed on Earth, Mockingbird was revealed being the Skrull Queen Veranke, who knocked Fury, Black Widow, and Quake with a laser rifle.
Maria Hill arrived to Fury's hideout and put Veranke to flight, allowing Fury to help Iron Man to repair his armor after Veranke transmitted a virus into it.
Fury is latter seen in the Avengers Mansion after the Skull invasion at Washington, D.C. was stopped by the Avengers.