Taken quite directly from page 5-8 of chapter 52. All are direct quotes from the manga; I've only novelized it and added depth to reactions/thoughts.
There was the sound of liquid trickling into a cup. "Care for a drink?"
"I am fine." His voice was of normal volume, tone soft, still formal, still distant, but the mind was sharp, weary but sharp. He was thinking, thinking, thinking about all the shit that was now on the walls and the big heaping pile he was sitting upon. All his plans, all his goals, his dream… He was on the verge of feeling defeated as he sat there in the opulent guest chair of the Fuhrer's office.
"Come now, there's no poison in it." Roy could detect both the amusement and seriousness in the Fuhrer's tone as he played to Roy's paranoia.
"Why, am I to make use of my life and sacrifice it here in this office?" His voice was almost resigned as he leaned forward with elbows on knees, clasped hands brutally squeezing each other. Everything he's ever known to date was replaying through his head and all ended in this tragedy.
"It is only for the sake of reaching a mutual understanding on your viewpoint," came the completely composed voice around a sip of tea. So in other words, Roy knew, until his loyalty was examined and his cooperation assured…or forced. In any event, he would be dealt with.
"…How long?" he questioned, voice tight, desperately trying to keep it from breaking. Too many things were clicking into place. "For how long have homunculi been able to string along the military as its head?"
"We have been constructing from the time of this country's birth. You know that." Another swallow of lightly steaming liquid, the privilege of he who controlled and delivered such calmly stated factual secrets.
"All this time you watched on chuckling as we struggled?" The bitterness ballooned in his chest. The anger was still there, still very strong and apparent to the both of them, but it was kept from his voice, from his words; visible only in the tense posture he held on the chair and of familiarity.
"Your hands were shaking at Brigadier General Hughes's funeral. It was nothing but a fabricated lie, was it…?" Such raging words, such clam delivery, such a despaired whisper. He felt he would lose the battle against the tears.
"You make such a commotion given the one death out of the number of men in the military." The teacup was in hand as he gazed out his window, taking in all the personnel moving about below, errands and tasks being executed in moderately timely manners. "From the time you accepted and donned that uniform, you should have understood the likelihood of your being buried in it."
A test was in order; another one. "Brigadier General Hughes's child… How do they call her…" he baited. "Well, be what it may, this one was not above such boisterous actions in the middle of the service." He further dangled the squirming worm before the already belly-up fish. "In all honesty, it really turns the stomach."
"You have a child yourself, as well." The formality slipped. Now his thoughts were on Gracia and Elysia and how their initial hardships had so many darker meanings piled atop them, now. He was angry. He was really pissed off. "That's something you should understand well!"
"A child…you mean Salim?" Bradley breathed into the window. "That one is a well behaved child."
Roy threw a sharp glance from the corners of his eyes, intending for added scathing to his remark. "I wonder if a homunculus can even know how to become what a respectable and model father should be."
Bradley took in that below him, the wide window quite an advantageous view of the premises, processing the boy's words and meanings. "Is that I threat, I wonder?" His eyes moved to track a laughing female secretary and companion. "Such things are pointless. That can never become a weakness."
Ah, how proud he was of his little prodigy alchemist, but the child needed to be put in his place. He focused his features and turned to his guest. "However, I would worry about myself, Colonel Roy Mustang."
Good. The boy's eyes and slightly agape mouth illustrated the uncertainty of what would be lorded over him. Foolish child, he already knew how to parent, had had years of practice. He preferred them well trained and already steeped in acceptable behavioral patterns; that's why he ran a dictatorship. But his favorite son – this brilliant, blessed, endearing, troublesome boy – this alchemist most supported by his hand was currently lacking in that area and now came time to re-establish the proper command structure. Some discipline was in order and he was a believer in strict punishment. Oh, Roy Mustang would feel the sting of this reprimand for quite some time in light of the seriousness of his offense.
It was delivered.
He had begun to almost want to worry when the boy's fallen face and collapsed chest had ceased to pass breath for some time, but the choked gasps soon emerged and rendered possible action moot. He stood directly beside the boy, even then the breathing quiet. "—this is the said conclusion drawn. How unfortunate, Colonel Mustang."
The boy was not broken, not yet; that he was saving. It would be vital later. For now, the angle he was bent would sustain them until the final twist to snap him came.