Disclaimer: Legendarily Quiet does not own Fullmetal Alchemist

In the end, things resolve themselves, and it happens in three steps.

One: Cassandra can't follow through with running away and turns herself in (Anna is adopted by the Hughes family).

Two: Herbert creates an antidote for Edward.

Three: Well, that's up to Roy to figure out.

Roy and Edward have some sort of heart to heart (which I assume is the climax?), and with Edward cured, things go more or less back to the way things were before. Only Ed doesn't insult Roy as much, and sometimes the colonel is openly affectionate or parental (patting his head, throwing a sandwich at him, trying to enforce a curfew, etc.) Both would deny that anything is different between them, although it's super obvious and Roy does admit to Riza in private that Ed may as well be his son now. Or something.

And if Ed and Al crash at the colonel's house instead of going to the barracks in-between missions, Roy doesn't say anything and simply dishes up an extra serving ("what, are you telling me you would've eaten all this by yourself? I didn't know you were such a glutton, Colonel!")

That's it.

If anyone is interested in adopting this fic – a questionable endeavour indeed – feel free to PM me! Or not. You could just take it and start writing. But give credit. Please.