It's set after they beat Loki, but before they send him back to Asgard.
SHIELD does some medical scans and stuff on Loki, and discovered something odd about his bones? (i think). That even though he looked like a fully grown adult, according to the scans of his bones... he was still in his mid-ish teens. And that he had apparently been pregnant.
So, knowing the Norse legends, they do some checking about and discover that some of those legends are horribly, horribly, true.
I can't remember much else about the story, including the name or author, but I am 100% certain I read it on AO3 (whether it is still there or not).