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2026-03-04
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Shepherds of a Dying Flock | Transformers Prime

Summary:

The Autobots and the Decepticons are the front-facing factions of the Cybertronian civil war—a conflict that has spilled out into the vast intergalactic and continues to destroy everything in its path despite the destruction of Cybertron.

That isn’t to say they are the only faction. Before the fall of Cybertron, a group known as the Shepherds of Polyhex took up the unique responsibility of trying to save as many lives as they could, N.A.I.L., Autobot, Decepticon—anyone touched by the conflict. After the Exodus, the Shepherds spread across the galaxy, with their leader and a small band of Cybertronian’s taking refuge on Earth.

Peace from distance does not last long, and ghosts of the past have returned to collect their dues.
________________
Self-indulgent, self-insert rewrite except it's a whole team of Cybertronians who have basically taken up the responsibility of cleaning up everyone's mess. Too bad said Cybertronians are plenty messy themselves in terms of their personal lives.

Notes:

(See the end of the work for notes.)

Chapter 1: Prologue

Summary:

Set in Season 2-- not at the beginning of our story.

Chapter Text

The Autobot base was suspended in a quiet tension between Agent Fowler and Optimus, the Prime’s battle mask withdrawn and expression in a rare scowl as Agent Fowler glowered back up at him.

“Agent Fowler, do you mean to tell me that the United States government has been harboring Cybertronian refugees, and have since neglected to inform us?”

Fowler, for his credit, stood his ground. The implications of the transgression were clear; and had Cybertron been a recognized country on this planet, the United States would be in a rather shitload of trouble.

But as it stood, there were a few fundamental facts of the situation that protected the United States—and Fowler— from the wrath of Cybertron’s Prime:

  1. Cybertron was not a recognized nation state of Earth.
  2. The Autobot forces were indebted to the United States.
  3. The aforementioned Cybertronian refugees were not only there first, but were not indebted to the United States. Quite the opposite in fact, as the small group of NAILs (Non-Aligned Indigenous Lifeforms) as they had identified themself based on faction alliance held the respect and favor of NATO.

“Well Prime, since I doubt the first come, first serve argument will please you, I regret to inform you that said group of refugees is in better standing than you Autobots with the international community of military leaders.” The agent crossed his arms, glaring up. Frankly, sometimes he envied the other liaison— at least Agent Calloway had genuine fun with her job. “They’ve been cleaning up your messes.”

“Wait wait wait,” Miko—who frankly should have not been in the room and should not be privy to international special intelligence such as the existence of the other Cybertronian group— stepped out from behind Bulkhead’s pede. “You mean to tell us there are more ‘bots?”

Fowler barely represses the urge to lecture Miko about the fact she should not be present for this conversation.

“Prime stationed his own group out in Maine, but yes. There is another group, but they aren’t bots. They’re NAILs.”

“Except for the very fact they are not!” Ratchet interrupts, stepping forward. “NAILs stands for Non-Aligned Indigenous Lifeforms. The Shepherds of Polyhex are certainly not non-aligned.

”Well they sure aren’t ‘Cons.”

”No, they are not,” Optimus gave a warning look to Ratchet, curbing any further argument from the medic for the moment. “However, the Shepherds of Polyhex are unique in their status. Given your favor toward them, I doubt you know the full extent of what they are and how they came to be.”

”I know enough.”

”Shepherds are built from former Decepticons within their ranks, your information may be biased—”

”Shepherds are also the group that’s been busting their asses since Korea to minimize casualties, and when you lot showed up, informed the United States that harboring you would come with risks, but would not violate any of our pre-established agreements and alliance with them. So honestly, you might want to thank them for saving your sorry asses or else we would have requested their deployment to turn you away from the United States and Earth as a whole.”

Silence returned to the base, and the other two human children made their presence known.

”…What exactly is a Shepherd?”

Ratchet turned his helm in the direction of Raf’s voice, exasperation clear on his faceplates. “I thought we told all three of you to stay out of here?”

”And when have we ever been known to listen?”

A valid point to be raised by Miko. The human children rarely listened.

Optimus’ faceplates schooled themselves into a neutral expression before looking at Ratchet and nodding. “Given the fact the Shepherds have elected to finally make themselves… known… I have reason to believe they’ve been involved in our activities for quite some time… Perhaps dating back to my treatment when I had contracted the Cybonic plague.”

”That… Would make sense…” Ratchet looked over to Fowler, glaring. “Can you confirm that your ‘contact’ was in fact a Shepherd?”

Fowler crossed his arms, “Yes. In fact, I called in a favor. And Prime came back in one piece.”

Ratchet sputtered, gearing to start an impassioned argument before Jack interrupted.

”Hey, as Raf asked earlier, what is a Shepherd?”

Ire at Fowler temporarily aborted, Ratchet turned his attention back to the human children. “A Shepherd, is a member of the Shepherds of Polyhex… A neutral but certainly Decepticon friendly faction back during the War for Cybertron. They skirted consequences and accountability for their actions through wartime ethical principle loopholes…”

”…So they’re not Decepticons or Autobots?”

”No,” Ratchet replied, shaking his helm. “The Shepherds are an alliance of medics. Neither side will harm a medic due to jus in bello, their leader doesn’t exactly do negotiating so taking a Shepherd hostage is unproductive.”

“How do you not negotiate?”

“The leader of the Shepherds in an unidentifiable femme… The only identity she does have is a moniker granted due to her actions. Actions that will never be brought to justice because of the earlier mentioned loopholes that Shepherds like to exploit.” 

“What Doc over there is talking about— since he seems to like to skirt around the grisly details,” Wheeljack interrupted, rolling his optics from where he was leaned against a stack of crated supplies, “is that their leader is a vigilante who hunts down either side for major grievances against wartime ethics… Wreckers and a few members of the brass especially seem to be on her scraplist.” 

“Well, Wheeljack, would you like to give the debrief then?”

It was likely unexpected that the weapons engineer would actually take on the task, but Wheeljack had always been full of surprises. Straightening his posture, he cocked his head to the side before transforming to alt mode, popping open a door.

“Alright kids, hop in… We’re going on a drive while the adults argue some more.”


Wheeljack doesn’t frequently utilize his altmode, he prefers root mode and the best mode of transportation is his ship. Besides, it wasn’t the most comfortable for three kids, but Rafael crawled into the backseat and made it work given his stature. Miko claimed shotgun and Jack took the driver’s seat by default, though Wheeljack had no plans of being pulled over. 

Driving down the dusty backroads of Jasper, the Wrecker takes a few minutes to collect his thoughts. The Shepherds of Polyhex were a complicated subject… And a deeply personal subject for any Wrecker. The formation of the group had been solely their responsibility. 

“Wreckers were given the more problematic tasks of the Autobot forces,” he starts, voice crackling over the stereo, “The sort of things that if it weren’t for the insignia, you might figure the group for a band of Decepticons. Not nice stuff. A long time ago, our commanders, Prowl and Ultra Magnus, had ordered the hit on Polyhex. It was… It wasn’t a good call… Too many civilian casualties, but the amount of Decepticon activity there made it inevitable… Optimus hadn’t been happy about the call.” 

“What’s Polyhex?”

“Ah, right. You kids don’t know much about Cybertron. Polyhex was a city in Northern Cybertron. Primarily a flier city. Not as shiny as Vos, the seeker capital, but it was the communications hub of Cybertron. After the hit we managed to take it and occupy it for only a short amount of time before Megatron had it destroyed.” 

“Were you there? Was it a big battle? Did you kill a bunch of ‘Cons?”

“I wasn’t there. I declined the mission. Quite a few Wreckers did. Bulkhead hadn’t joined yet and while Breakdown was part of the Wreckers unit at the time, he was out in Velocitron trying to convince his conjux to defect from the Decepticons… Ironically the opposite happened.” 

“Breakdown was an Autobot?”

“Yeah,” Miko answers, leaning back. “Bulkhead told me all about back when he got captured by M.E.C.H.”

“But yeah it was a big battle, but it wasn’t Decepticons that ended up paying the price. It was civilians. The only notable victory was taking out the Deception CMO… I did, however, feel the after-effects.” 

“...So if you guys destroyed Polyhex,” Rafael speaks up from the backseat, leaning forward toward the stereo system, “why do the Shepherds exist?”

“The Shepherds were a direct result of the hit on Polyhex, at least, the Shepherds that they’re talking about back at base. Previously, the Shepherds were a group that was evacuating out civilians from Cybertron, getting them set up on offworld settlements and planets that would offer Asylum… Their main base of operation was in Polyhex and Megatron seemed to grant them a very unique leniency. Prowl figured the Shepherds were working with the ‘Cons and that was the only reason why, but we never got confirmation on that and if Optimus knows something, he hasn’t shared it with the class.” 

“After what happened on Polyhex, they had a new leader. I assume their original leader, a femme by the name of Oracle, must have been killed in the attack. This new leader was… Well, let’s just say she was brutal. A summit was called between the leaders on neutral ground. Megatron, Prime, their seconds, and the new leader and her second. I read the report, but essentially it established the requirements for ‘Just War’ within Cybertron. Did two things really: established combat immunity for medics—which both sides benefited from, especially the Decepticons after the loss of their CMO—and granted a ton of permissions for the Shepherds to operate for evacuation capacity and defense of civilians and patients…”

“None of that sounds brutal.”

“It wasn’t. Until the Wreckers started being killed off.”

The car goes silent as the children process the answer, trying to make the connection. Wheeljack won’t put them through the mental gymnastics, so he continues. 

“I was there for the next hit, we were instructed to attempt to take out Helex—another city. Everything was going to plan and then all of a sudden Motorsight’s helm was rolling on the ground, detached from his body. Everything went to scrap after that. Took us stellar cycles to figure out what was going on, and then kilocycles to figure why. And when we did, we realized that the summit had all but granted the Shepherds diplomatic immunity… We couldn’t go after them.”

“Their leader got her designation—well really an alias—because we managed to upload memory files from one of the Wreckers she killed. No bot knows what she looks like, not even the big guys—”

“How can you do that? Was she like that ‘Con that pretended to be you?”

“Oh no, Makeshift was something special. She used an optic disrupter—er… a disguise— during the summit. But the memory files revealed that the killer had a red paint job, so our killer got the nickname ‘Red Death’. Or, at least that’s what it translates to in English. It’s a bit more threatening in Cybertronian vernacular.” 

“I think Red Death is plenty threatening,” Jack replies, tapping his fingers idly against the wheel as another car passes them by on the road. 

“Fair enough. After the blurry image got disseminated between Autobot and Decepticons alike though, she started taking the helms with her to prevent memory chip uploads. And then we found out she was killing from both sides. Equal opportunity I guess.” 

“So that’s why Shepherds aren’t Cons. They kill them too?”

“No, Shepherds aren’t Cons or Bots not because of who they’re killing. A Shepherd’s primary objective based on supplemental coding is to protect and treat a patient. Most of the time, those patients are civilians or NAILs. On occasion Decepticons or Autobots. Decepticons are rather appreciative of medics regardless of their alliances so they’ve been known to physically defend a Shepherd found on a battlefield. Autobots less so, because we figured out their leader was picking off Wreckers before the Decepticons did… And besides, Decepticons already had a Justice Division, half of the people they were picking off were from the damn hit list but that’s a story for a different time.”

“Hit list?! You mean Decepticons were killing their own?”

“Story for a different time, Miko.” 

“Right, okay.” Miko leans back in her seat. “So if their primary objective is treating patients, why did they start killing you guys?” 

“That’s the why question. It took a while to figure it out, but eventually we found a pattern. We didn’t even realize it was a Shepherd at first until the image had been enhanced enough to make out their insignia. Then Prime reached out to their leader and in response got a big ol’ data packet.”

“A data packet? Really?”

“Yeah, casualty counts. The Shepherds had been tracking casualty counts. By that time, just about every Wrecker directly involved in the hit on Polyhex was dead.” 

The kids go silent, a moment of mourning for Bots that surely would have been great additions to their current team. Or at least, Wheeljack assumes Miko would think so. Wheeljack honestly couldn’t say for sure if the Wreckers involved with the hit on Polyhex would have been well suited for how much had changed. 

“...Prime and Prowl had parsed through the data and found the connection in a couple vorns,” Wheeljack continues, “other than the Wreckers from the Polyhex hit, any time a Wrecker hit a certain number of civilian casualties, they ended up on the Shepherd hitlist. Communication between Prime, Megatron, and that leader confirmed a few things. But mainly that the one killing them was her. And that they had legally permitted her actions through the immunities and privileges granted at the summit.”

“Well Prime didn’t stand for that, did he?”

Wheeljack goes silent for a few minutes. 

“Did… he?”

“He didn’t really have a choice. It’d take too much resources to track down the leader, resources that were needed for the war. And any Spec Ops mission to track her down had failed spectacularly. Not even Jazz could get her. And while I wasn’t privy to those reports, I could read between the lines. The Shepherds were also widely non-violent, and had the favor of most Decepticons, so we risked losing a whole legion of medics willing to aid anyone by going after their leader for dishing out justice…” 

“But come on, Megatron couldn’t have allowed that!”

“Megatron was in a similar situation as Optimus. And again, that Justice Division and Red’s hit list had a lot of overlap. Both factions seemed to issue the order of keeping civilian casualties down as much as possible—easiest solution. Which meant us Wreckers were repurposed to just straight wrecking things in areas that were purely Decepticon and Spec Ops got a bigger workload.” 

“...Did you guys really kill that many civilians?”

“...Much of the Autobot forces were built from Enforcers during the previous age—when the Senate was in charge… I can confirm the number for those who were killed was pretty high. But none of us on Team Prime has gotten close to it yet.”

“That’s… Relieving.”

“Death and casualties are part of war, kiddo. Neither side has enough soldiers to really support a full blown war here on Earth at the moment, but that might change with time… I just hope it doesn’t.”


“Agent Fowler, I believe I am understandably justified in my anger toward your failure to disclose the existence of a Shepherd faction on Earth.” 

“And I am understandably justified by my position as an agent for the United States to not disclose that information and put international alliances at risk.” Fowler headed for the elevator door. “And I got news for you pal, the Shepherds of Polyhex have the right to call in any favor they want. Including a dissolution of our agreements to harbor you. So again, you might want to have some damn appreciation.” 

Optimus held back the words on the tip of his glossa as Fowler punched in the exit code to the base and entered the elevator. He maintained his silence until the proximity sensors had confirmed the lift-off and complete exit of the agent. 

“Optimus?”

A heavy ex-vent left the Prime as he turned to face his team. “...We will not engage with any Shepherds… It’s quite clear they have extended aid and neutrality to our own forces during our times of duress, though we were unaware of it.” 

“That doesn’t mean they haven’t extended the same to any ‘Cons.”

“Shepherds tend to operate with the objective of not being seen nor heard, Arcee.” Optimus glanced over to the monitor, almost considering reaching out to Megatron for confirmation of whether or not a Shepherd had been spotted in aid of a Decepticon. Just to get a better grasp on what the situation might be. “Besides, we cannot confirm that their leader is also present here on Earth. They are spread across the cosmos as much as we are.”


A dark plated seeker tosses a bite sized cube of jellied Energon into her intake as she watches the monitors from her seat. She had to go handle a minor emergency in the medbay—their new patient’s critical condition—so she is roughly 30 minutes behind the live feed, but she’ll catch back up when they all go back to recharge. 

“For Pete’s sake, Autobots are dramatic as all hell.” 

She glances over at Agent Calloway who’s leaning over a platform that puts her eye-level with her Cybertronian assets. Despite the human’s lack of EM field, she can sense the stress and anger from the agent. A blackberry phone—government standard—is still being tightly gripped. If the Cybertronian had to guess, Calloway just got off a call from Fowler. 

“You can say that again.” The femme takes another small cube of Energon and averts her eyes back to the monitor. “You’d think with us saving their asses… Three times now?”

“Three.”

“Yeah, you’d think with us saving their asses three times now, they’d have a bit of appreciation.” 

Pedesteps echo down the hall. The seeker communications officer only leans back slightly in acknowledgment as another bot steps into the entryway of the surveillance room. 

“Everything stable back there?”

“Yeah, the patient's stable.” Pedesteps and an encroaching EM field full of equal parts tension, exhaustion, and relief indicate the room has been entered and now the bot stands directly behind the seeker. “Anything interesting?”

The femme shrugs, spinning her chair and trusting Calloway to maintain surveillance as she faces the other. She’s not that worried about Autobots storming their vessel, but Decepticons are still up in the air. Literally.

“Well, they don’t seem to be considering any drastic action.” 

An optic ridge raises in skepticism, “That’s rather out of character, drastic action is practically their calling card. Especially with the mechanisms in that particular team.” 

“Yeah, well, they don’t think you’re here.” Calloway remarks, glancing back as she shakes her phone. “Fowler was smart to keep from mentioning any of your names explicitly. Granted, I think the only one that might get semi-positive reception is Jetfire.” 

“Ah,” a red servo reaches out as the femme steps further into the room, moving to the monitor. “Well, I can’t say I’m surprised by that. But extend my gratitudes to Agent Fowler for his discretion.”