Say in a new story a new hero and villain were introduced into the Marvel universe but their dynamic was very like the villain was viewed in the eyes of the public as a hero and not just a hero was also like a son to Nick Fury, an Avenger and pretty much like the best friend of each Avenger and tight with each one. But underneath the facade of heroism was a very evil person that ran his own terrorist organization and committed crimes like weapon, drug, and human trafficking and even sold S.H.I.E.L.D. secrets under the table like the world terrorist version of Wilson Fisk.
And the hero ends up on this Villain's radar by being an unfortunate witness to his crimes and after surviving an attempt on his life develops super powers but has to go on the run after being framed. Ultimately this hero has to dodge SHIELD, the Avengers, and the Villain's own group. Basically like the movie The Fugitive with the truth not being revealed until it's to late but Fury ultimately ends up suspecting something is up (but is too blind to see the Villain's true nature) with the villain the truth coming out in a all out confrontation similar to this.
How do you think Fury and the Avengers would react in such a situation where they learn they've been fooled into the fighting the real hero and tricked by the real villain into doing his dirty work?