There are only a few people Nick Fury really trusts. One of them is Clint Barton. Despite having his brain hijacked by a God, Nick's trust in his archer never wavered.
So when Nick finds out about Hydra, he sends Clint to keep an eye on the remaining Avengers and track Hydra threats. He tells Clint about Hydra's infestation of Shield and tells him not to tell any other Avengers. While Clint doesn't like it he keeps it a secret.
Then Clint begins tracking Hydra threats within Shield. He tells the Director who to trust. He also tells Nick he is suspicious that someone from the WSC is Hydra.
Clint is busy blowing up Hydra bases when he hears Cap and Nat are fugitives and that Fury is dead. He knows its begun and Nicks too smart to be dead.
2 days later Maria calls him and tells him he can take a break from his mission.
He reads about how Nat leaked all info on the Internet so he decides to go comfort his girlfriend.
When Nat tells him everything, he tells her about Nick approaching him and how he already knew. Nat's less than happy but accepts his explanation when he says he wrote everything in a letter if something had happened to him.
With all their Shield houses compromised, Clint and Nat go to his family farm to recover before Avengers are needed again.