It nearly broke Kakashi's heart when he realized who the boy was.
The history of this universe is that, after Fullmetal Alchemist the anime (not manga, which is a whole different can of worms) ended, the military dictator-esque government was dissolved and a Council of multiple civilian leaders was set up, with a separate position for a military leader called Commander General, abbreviated to Commander, that held a seat on the Council and as the highest ranking officer. To become a State Alchemist it is required that the Alchemist train under/apprentice themselves to a certified State Alchemist for a period of at least a year or until the teacher recommends them before they can take the exam. They can sign up for this apprenticeship, but most of the time the students are invited through State and Council selection.
Disclaimer: I do not own Fullmetal Alchemist and am not making any profit by writing and posting this story.
It nearly broke Kakashi's heart when he realized who the boy was. And then he seriously considered sacrificing his body to bring the bastards who had done this back to life, to have the opportunity to kill them again with his own hands. Maybe he'd ask them how they'd done it while he was at it, incase there was something he really should know about the boy's physiology – because for goodness sake, a Chimera who can do alchemy has got to have some Trojan horses in their DNA.
The Commander kept an eye on the boy, of course. The only eye he had, actually, which served well enough. Kakashi trusted Mustang to look after him, especially with how the two were connected. Kakashi still tried to convince the man that Edward's death wasn't his fault, and Roy still tried to convince Kakashi it wasn't his. Neither man had much success.
But the Chimera boy who could use alchemy (Edward's son, as he'd discovered. Kakashi wondered if Roy hadn't told him who his charge was on purpose, or if he just didn't want to talk about it.) had touched his heart. He was fun-loving and protective and had the potential to become great, and he held Kakashi as one of his precious people when he'd done anything but deserve it.
Kakashi couldn't quite wish that Mustang had put the boy under someone else's tutelage.
"Naruto, you idiot."
The other two, well, that was another story. Kakashi spent every second that he trained the brats wishing he wasn't where he was. He wished the girl wasn't so god-damned smart so that she wouldn't have to be here in the first place. He wished that the dark-haired boy with the haunted eyes hadn't listened to his arrogance and attempted Human Transmutation. Most of all, he wished that if his first two wishes were unanswerable, that he'd have never taken the job of Sensei for potential future State Alchemists in the first place.
Yeah, right. He'd been conned into that by Head Councilman Sarutobi himself – he hadn't stood a chance.
"I'm not an idiot, bastard!"
"Naruto, don't call Sasuke a bastard!"
"But Sakura, he started it!"
"Maybe the two of you should just kiss and make up." By the faces they made and the disturbingly green color their skin turned, Kakashi figured he'd gotten through to them. "Now then, you have no cause to be fighting. Do you want to know why?" Kakashi smiled gleefully and didn't bother to wait for an answer, he just pointed down at the table where the array they were bickering over was drawn out. "You're both wrong."
Funny. They all looked like they'd swallowed something sour.
Kakashi tried not to grin in amusement, and decided that now was the perfect time to leave his students hanging. Maybe their joint hate of him would prod them towards teamwork and they would work together to figure out the array he'd drawn.
Kakashi teleported away. Then he sighed at himself. He needed to stop reading romance novels, if he was starting to think like that. Those kids'll never have a happy ending.
He didn't realize until later the painful truth of his own thoughts.