Usual disclaimer, I don't own Fullmetal Alchemist and it's characters.

"What undercover?" Ed did the unfortunate thing of not listening to a mission briefing once again.
He was now twenty, got his brother's body back from the gate and he got his right arm and left leg back. With his original goal completed he decided to stay in the military much to everyone's surprise, even Alphonse. The boy matured into a young man, promoted to Brigadier General he could have his own team, but refused, staying with the original setup he was used to under the new General Mustang, Hawkeye, Breda, Fuery, Fulman and Havoc. His height was no longer an issue, within two years of getting their bodies back he was now almost the same height as the general, he was still hoping to grow taller to finally take revenge of all the short jokes that he pulled over the years.
Mustang glared at him "Fullmetal this is a very important mission, the lives of all Amestrians rely on the outcome of this." Ed kept his state title, he was offered other names when he was re assigned, but felt a need to keep it. It was how everyone knew him after all.
"Sorry general, my mind just wandered off..."
Roy sighed as he repeated himself "Intelligence have found a small group of rebels plotting to destroy this country and everyone in it.."
"So I have to capture them, no problem.."
"It's not that easy Edward.." Hawkeye speaks out from behind him "..if one gets captured then the citizens will be killed, they need to be captured all at once."
"So just tell me where their hideout is then.."
"As soon as intelligence tracks them down they have already moved on.."
Ed looked back to Mustang "So that's what the undercover bit was about?"
Roy stood up and went to the window. "You'll be working with me on this assignment Fullmetal, I need you to be in disguise. The leader of this group hangs out in a well-known bar, which I happen to frequently visit, so me being there won't be an issue. The government recommends the military personnel to avoid this bar as it is crawling with criminals."
Riza suddenly interrupts "Which makes you look like a criminal yourself, no matter how much I persuade you not to go there. People there would think you're corrupt."
"Even better for the situation, thank you major..but Edward, I need you to be undercover, just you walking in as you are would cause uproar. So me and the major talked of several scenarios which might work. We decided on one...I'm not brilliantly keen on the idea, but it is our only option."
The blonde scratched the side of his head "Okay, so what do I need to do?"
"We need you to go a woman."
"WHAT!? No way in hell, why do I have to? Why not get the major to do it"
"Hawkeye would be noticed in seconds, you've kept under the radar ever since you lost your alchemic powers. Most people think that you've left the military and gone back to Resembool. With a bit of alteration you'd be unrecognisable. Yet we don't know how long this mission will take, we've been excused from any other assignments until this one is complete. The major will help you with your disguise."
"So what is the point of disguising myself as a woman?"
Roy paused for a moment and looked back from the window towards the man sitting in front of his desk " You'll be disguised as my fiancee, this being that you being with one of the highest ranked military officers would get you access to top-secret information. We are hoping that they contact you concerning this...and if they don't well, you'll have to make your way into their ranks. I wouldn't ask you to do this if I didn't trust you Edward.."
Ed just sat there looking at the floor, he would be putting his life on the line once again for Mustang, for the citizens of Amestris. All he had done the past two years were help with information gathering. As much as he wanted to go out and inspect areas like he used to, he knew if he ran into trouble he didn't have alchemy to help him. Sure, he knew hand to hand combat, but that would only get him so far. The general did offer him assignments out of the military building, but he was just more than happy helping Roy with his work.
"Well...I guess it'll make a change from being in the office all the time...and to see if you still got it Mustang, it's not like you've been on a mission for a while."
Roy was surprised how easy it was for Ed's acceptance. "Well at least I'm not doing as much paperwork as I used to, since you're not out destroying everything."
"As much as I don't like the idea of disguising in that way, if it's to save this country I'll do it." Ed's determination was clear to see, he did miss the thrill of dangerous assignments. "Just...don't tell Al and Winry about this..."
"Us three will be the only ones who know of this plan as to not endanger you. You and Major Hawkeye go to my house. Hawkeye, make sure everything is prepared for tonight, I'll meet you at home when my work here is done."
"Yes sir" She took his house keys and left the room with Ed closely following behind.

Roy stepped through the door hanging his jacket on the nearby clothes peg.
"General sir, we are nearly ready, go get yourself changed." Riza's voice echoed through the halls from the backroom. He sighed as he slowly climbed up the stairs he at least wanted to take a little rest before they headed out to the bar. His was curious as to what Edward looked like dressed as a woman, but knew if he didn't get a move on his Major wouldn't hesitate to make him look down the barrel of her gun. Opening his wardrobe choosing a dark grey suit, ignoring the darker waistcoat and black tie. There was no need to dress smartly leaving the top two buttons of his shirt undone, it was a look the women couldn't resist. For a moment he forgot all about the assignment he volunteered for and wondered how many woman he could get, to realise for a while he'd have to be a one woman man, and that woman was a male subordinate. He walked back downstairs to the back room door, knocking gently awaiting instruction to enter. Receiving no answer he remembered that he was in his house, why did he have to ask permission to enter his own room? Quietly opening the door he saw Riza behind Ed helping him keep his balance.
"Come on Edward, just like I taught you.."
"How do you women do this? It's impossible! Can't I just wear flat shoes? I'm bound to be taller than Mustang wearing these, it'll look too weird!"
Roy quietly closed the door and leaned against the wall. He couldn't see Ed, but it was amusing enough just to listen to him complain again.
"I suppose you're right, let me go and get them.." She turned round to see Roy looking as handsome as ever "Sir, you can sit down you know, we are almost done."
She walked out the room and the Flame Alchemist stared at the back of the person left standing."Turn around Fullmetal, let's see what you look like."
He turned round as commanded with a slight embarrassed blush across his face, to Mustang's astonishment he looked like a completely different person. The once blonde hair was a dark brown, the center parting and bangs were gone, instead a side parting with his fringe swept to one side of his face covering his left eye. Those eyes..the once golden orbs had now changed blue.
There were hints of make up, but not a lot at all. Complete with a pastel blue blouse and black pants, his broad shoulders were disguised well under the black jacket ...if he didn't know that the person in front of him was Ed, he'd probably be hitting on him right now..
"Wig, contacts, padded.." Pointing to his chest "..have to say, the major did a pretty good job." He nervously smiled towards the man, who was wide-eyed and with his mouth open in shock.
Hawkeye walks back in with a pair of flats for him "General, please put your eyes back in your head and close your mouth.." She handed the shoes to Ed "..from the look on your face I guess the disguise is suitable?"
He coughed, suddenly snapping to his senses "It is acceptable, thank you major.." She smirked towards Ed, this was the reaction she'd expected to get from him, after all she had just created Roy Mustang's ideal woman.

They all sat down going through the last details required for the mission. Roy was still in disbelief, if anyone else walked through the door they would just think that he was another one of his women.
He was once again snapped out of his trance "Yes, sorry Lieutenant.."
Ed smirked, his disguise must be that good "General I need renaming when I'm dressed like this, you got any ideas?"
"Well, um...I guess Edwina?"
The others glared at him, so much for his help.
"General the idea of a new name is that it doesn't sound like the original, you'll blow Ed's cover and the operation, your lives will be at risk not to mention the whole country." She sighed as she turned back to Ed "How about Elizabeth?"
"It'll do, I'm no good with names" Ed nervously smiled as he looked up to the clock.
Roy stood up and headed towards the door to get his coat "It's about time we got going."