Fury is pissed off to find that everyone thinks Tony Stark is the leader of the Avengers after the Battle of New York.
He tries to set things straight.
It doesn't work.
While Tony's considering pulling in Spider-Man, he spots someone in the background and changes his plan.
He meets a woman who has been networking with New York's enhanced, and gets him a (mostly) unbiased team to pull in the Rogues.
With an organisation like S.H.I.E.L.D. around, some people will go to all sorts of lengths to keep their people safe.
Especially when they've seen, first hand, just how bad it can get.
(Expansion of Security.)
When Team Cap "fight the bad guys", they pay no attention to their surroundings.
It comes back to bite them in the butt.
And, this time, they've gone so far over the line that Tony's not helping them.
Over the years, SHIELD has whittled down Earth's natural defences (who they called the enhanced) down to sparcity.
So when Thanos arrives the Transcendent Souls make a clear decision on what to do about it.
And they know just who they need.