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It isn’t that Clint hasn’t been invited to join various organizations before (only one of which he has said yes to, for the sake of Laura and the unborn child she’s currently carrying). It’s that the man doing the inviting is so damn nice.
Phil Coulson is quite probably the nicest person Clint Barton has ever met. He could be loyal to this man, Clint thinks, if Hydra hadn’t gotten to him first. But Hydra wants him in SHIELD, so into SHIELD he will go, letting Phil think he’s the reason Clint said yes.
Not telling anyone where his loyalties lay until he’s ordered to, because while Clint Barton was definitely a good man, he was a family man first, and it was Hydra that was protecting his family from the outside world, from the enemies Clint had made since leaving the circus.
Hydra comes calling three days after Clint manages to put an arrow into the wall next to the Winter Soldier. It’s the first time Clint’s missed his mark in years. It’s the first time the Winter Soldier had been nearly killed in all the time Hydra has had him.
But when John Garrett catches up to him, with orders to kill the man that nearly killed Hydra’s best weapon, Clint is with Laura, waiting on the response of the pregnancy test, and John makes a different decision.
John, for all that he is a monster, has a soft spot for children, even ones that haven’t been born yet, and the test will very shortly show positive.
“You nearly killed our best man,” John said. “Marksmanship like that is rare, especially with a bow. I imagine it’s given you plenty of enemies.”
“More than a few,” Clint acknowledges.
“The organization I work for can hide them, keep them safe for you, if you come to work with us.”
“So you can use their lives to blackmail me into doing your bidding, you mean.”
“No,” John said, glancing at Laura’s stomach. “Not while I’m around. They will be safe, and you can see them whenever you want.”
“What organization?”
“Hydra. You might have heard of us before.”
“Yeah, I might have,” Clint said. He turned to Laura and they shared a silent conversation, that ended with Laura’s hand over her stomach. Clint turned back to John, “If anything ever happens to them, not even Hydra’s best man will stop me from killing every single one of you. Slowly.”
“Understood,” John said, holding out his hand. “Hail Hydra.”
Clint hesitated before grabbing his hand, “Hail Hydra.”
And so into SHIELD Clint goes. He passes all the tests they give him. He’s assigned to Phil Coulson. He goes on missions for SHIELD. He passes John Garrett in the hallways and they don’t acknowledge each other until Phil ‘introduces’ them to each other. He goes on more missions for SHIELD. He goes on missions for Hydra. He goes on even more missions for SHIELD.
And then he’s sent after the Black Widow. And he shows her the same mercy that John Garrett showed him.