Clint and Natasha join SHIELD as kids and Coulson takes them in.
I originally thought this story was "We Grew Under a Bad Sun" by torncorpse but though this is a good story and similar, it's not the one I'm looking for.
The story I'm looking for is complete. There's a scene where Coulson takes Clint to the zoo and Clint sneaks away on one of Coulson's missions and saves it which results in Sitwell getting a crush on him because he thinks Hawkeye is a woman.
Natasha joins them by being sent in a box and she kills some agents before Clint can stop her and asks to keep her because she's like him.
Clint and Tasha try the couple thing but find they prefer being siblings.
Bruce agrees to go with Tasha cause she says her brother was in trouble.
Clint gets men to follow him under Loki by letting them beat him up. Loki does not approve.
Clint gets his mind back sooner because said men beat him up and he flys to the rescue with something wrapped around his bleeding head causing Tony to snark about about his "fashion sense".
Clint pleads with Loki to save Coulson and become a good guy, which he does, and they all live happily ever after.
You'd think with remembering that much I'd find it but Google just isn't being nice to me today!