I'm a little rusty, since it's been a few years, but I would appreciate advice. I know this isn't canon, but it's what I wish would've been the story.
Disclaimer: I don't own Firefly.
The Shepherd
The minute the Operative's two ships broke atmo, Book knew his Haven was lost. He ushered the children into the basement of a building, but some of them refused to leave their preacher's side. One of the smallest, Kaylee's favorite, disappeared from view—Book knew he was hiding and would come out later, but time was short and the adults needed to be armed.
"Sam. Take these. Unlock the armory," ordered the Shepherd, throwing a set of keys at a nearby gawker. "Find as many people as you can to empty the place and arm everyone you see. Fast!"
The first ship began to shoot and the remaining adults ran for cover. Building after building burst into flame, the wooden beams collapsing onto each other and spreading the fire to the lower floors.
The children. They were going to burn alive. The Shepherd ran for the building that hid them, but he was too far to do anything as a missile drilled through it and then exploded, showering everything in a fifty foot radius with debris. Book stopped in his tracks for a precious second, mouth agape. He could hear the agonized screams of those not lucky enough to die on impact.
"Shepherd!" A gun was shoved into his hands. "One of their ships is land—" A new round of strafing cut Sam short. He fell at the Shepherd's feet.
Lord God, have mercy… The ringing gunshots stopped abruptly. Book turned, scanning the surrounding area for both the number of casualties and the reason for the ceasefire.
Out of the grounded ship came three men. Two sported semi-automatic weapons and immediately engaged the remaining Havenfolk. The Operative, meanwhile, strolled towards him, hands clasped behind his back as he surveyed the damage and stepped over bodies. He stopped a few feet from Book and half-smiled. "Shepherd."
Book did not reply.
"Your new home is much…messier…than the last. I prefer the old place. Less blood."
"Why, Tyler? Why are you doing this?"
Quick as lightning, the Operative pulled out his gun and shot the Shepherd in the stomach. Book stumbled back, clutching at the wound and trying to breathe and not breathe at the same time. He was a dead man. It would take time, but he was done. "We had a deal," the Operative reminded him calmly as he holstered the weapon. "You never call me that, and I never call you Father. Remember?"
Book could only gasp in response. He'd been shot before, but somehow, this was less painful. He still had to defend what was left of his home, and his focus blocked out some of the pain.
"I'm sorry, but you don't deserve an honorable death. The sword is meant for those who have done great things. You…you broke our family tradition. Ran, like a coward."
"I…I didn't…" Book looked to the skies for strength. "I just…found something else to…believe in."
"Something other than the betterment of humanity? Something that you could achieve by traveling the stars in a smuggling ship with the most dangerous of fugitives? I still cannot fathom that the man who taught me to stand by my belief was so easily shaken in his."
Book could no longer stand. He crumpled to the ground, still trying to hold the blood in. The Operative came closer and leaned in.
"Let's see how easily your friends' belief in you fails. Before Malcolm Reynolds dies at my hands, I will tell him everything. Tell him who my predecessor was, and the work he did for the Central Planets. I will show him the real 'Shepherd Book'. I'm sure he has questions. They will be answered. And your memory will forever be disgraced." He paused. "Forever. Perhaps I misspoke. Disgraced until I kill the crew and the girl. Then you'll be erased from memory altogether."
The Operative pushed Book onto his side and reached into his pocket, pulling out the Identicard.
"The Alliance would like this back. No need to allow scavengers access to everything."
"Tyler…you don't understand…what they will do…to that girl. Please. For once. Look at…the cause…you are helping."
"And there it is again. I'll let that slide. Good bye, Father. I'll let my soldiers finish off what's left here."
Shepherd Book waited until the Operative had boarded his ship and left the ground before pulling himself up. The gunfire from the ship that remained had resumed, although there was no one fighting back. The Shepherd struggled through the broken boards and corpses that had once been his friends. Only when he'd found an over-the-shoulder missile launcher did he start to worry about being spotted.
The ship was too far for him to do any damage from where he was standing. With what had become a permanent wince, Book raised the smaller gun given to him by Sam and fired three shots in the air.
The pilot turned the ship as fast as possible, and was soon within range of Book's weapon. Unfortunately, that went both ways, and the Shepherd was forced to crawl for cover before actually discharging anything. He had one shot, and just holding it on his shoulder was starting to seem impossible.
May God forgive me. He ignored the stabbing stings from his stomach and took aim.
Three seconds after he fired, the ship crashed with an earth-shattering quake. The Shepherd dropped the launcher and fell back onto the dirt, finally at peace to pray for those who'd lost their lives.