Taking place in Transformers: Prime, this short story brushes the ever loved idea of Megatron losing his memory and reverting to Megatronus. 
This takes place between Darkmount, Nevada and Evolution.

D-16 was the original name of Megatron when he was a simple miner in the Cybertronian caste system (before becoming Megatronus).

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     Optimus ducked as the mine collapsed, trying to evade his pursuer as the war lord cried out at his opponent.

         "The great Prime has become cowardly!" He taunted, but it effected Optimus little, the blue and red titan twirling in the confines of the cave to face his adversary before firing above Megatron with his machine gun. The war lord ducked, laughing as he stood up. "You missed."

         "I was not aiming for you," Optimus answered, watching as Megatron swiveled around, only to stare at the onslaught of rock from above. He was to late to escape the cave-in. 

     As the walls still crumbled and shook, Optimus neared the rubble, spotting a silver servo. Was Megatron finally dead? The Decepticon war monger, defeated by Optimus Prime? No, the servo twitched, and the lightly covered helm of Megatron lifted with a groan. Optimus readied his transformed canon, aiming at his long time enemy's helm as the familiar red glow of his optics peered up at him.

         "Orion, what- what is happening? When were you armed with canons?" 

     The panic in the gladiator's expression made the Prime's optics widen, and he transformed his servos back into view, holding one out for his friend to be pulled up from the rubble. 

         "There is much explaining to be done, old friend. Let us hurry, the cave is about to give way. Ratchet," Prime called from his comm, "we are in need of a groundbridge."

     The swirling portal appeared before them and Optimus acted as a guide for the gladiator. The tunnels collapsed behind them, dust surrounding their pedes even as the groundbridge closed in the military hangar. Both beings coughed to expel the dust from their vents and Megatron smiled thankfully to his friend, only to frown.

         "You've gotten taller..."

         "Why is he here?" Arcee held both canons steadily, aiming for the war lord's spark. 

     Megatron stood straight, unamused. He looked around, noticing the others were equally as on edge as this femme whom he failed to recognize, even the well known medical officer, Ratchet. The titan smiled at the orange and white mech.

         "Another familiar face! Ratchet, what is going on, I'm quite desperate for answers."

         "O-" Optimus raised a servo before Arcee could finish saying his designation. Megatron would know him as Orion, not Optimus.

         "Autobots, this is Megatronus, a long time friend," the Prime explained, "We were in the mines when part of it collapsed on top of him. Ratchet, I suggest examining his central processing unit." The medic nodded quickly.

         "Orion, I feel fine," Megatronus assured, "it takes more than rock and ore to bring me down, you should know this."

         "Of course I do, my friend, but you took a very hard hit."

     The titan complied, trying to joke with the doctor, but Ratchet merely huffed grumpily telling the mech to hold still. It was quite an amusing sight, but no one was laughing at it. The others kept their distance, all wanting an explanation from their leader.

         "Optimus, was this the wisest thing to do?" Ultra Magnus questioned first, "How do you know he is not merely faking this amnesia?"

         "It is rare to see a fear in his optics, and I recognized the fear of a long lost mech. Megatronus was not so adept at hiding it when around friends or trusted individuals." The Prime answered.

         "What are we going to do with him, then?" Arcee spoke up, "Tell him he's committed war crimes and trial him for things he's forgotten?"

         "Sounds fair to me," Smokescreen huffed, "When Optimus was an amnesiac he was used for his archivist skills, we don't exactly have anything we can use Megatron for other than point him against his own team."

     Bumblebee whirred, making a good point.

         "You're right," Bulkhead shivered, "seeing his team might jog his memory. He lost it because of rocks hitting his helm, not from a lack of the Matrix."

         "So, we can't tell him about the war at all?" Smokescreen spoke up again, "I'm surprised seeing Optimus didn't make him remember right away. I mean, he doesn't exactly look like he did as Orion, or even his old Prime state."

         "Memory loss can be tricky," Ultra Magnus informed, "I know several soldiers on Cybertron who would remember certain things but not others, or mix two different memories. In Megatron's mind, he may have drawn the conclusion that Optimus is Orion, and simply changed his appearance at some point in whatever time gap he may think there is."

         "He didn't recognize us, either," Arcee noted, "Yet we all know he's seen us at one point or another. If we don't know what exactly would reactivate his memory core, then would it be best to simply not tell him what's been going on?"

         "That would be difficult considering certain clues would later reveal it," Optimus shook his helm, "Megatronus was always a tactical genius, very smart and well learned in knowing how to read others." 

         "I can hear your compliments, Orion," said mech greeted the group with a strangely out of character smile, his red optics just as joyful, "but why do you speak in past tense? Ratchet is oddly cynical. I've always known him to be grumpy but he seems battle worn." The happiness melted into concern as he stood by his friend, glancing at the others as they took mild steps back. "You haven't introduced me to your group, either. Autobots, you called them?"

     There was an awkward introduction, and Optimus was skilled enough to avoid any possible looming questions Megatronus may have had about the ragtag team. The Prime soon convinced his friend that he needed recharge after his blow to the helm. Ratchet admitted later that it might not have been wise, in case the effect of amnesia wore off during the mech's power-down.

         "Hey Op-"

     Jack was interrupted by the eruption of 'Sh' from the group, everyone tense, and the three children more so as they entered the hangar. 

         "What's with the bad vibes?" Miko questioned.

         "It's a long story," Bulkhead answered, and Optimus provided said story. The three children stared at each other with wide mouths as their squishy processors took in the haunting information.

         "What happens if Megatron gains his memory back in the middle of base?" Jack questioned, "He's likely to remember me considering I kind of brought you back from your pre-Prime state."

         "He did not recognize me as my Prime self," Optimus shook his helm, "his anger towards you is not as great as his wrath towards me, so I do not think it is likely the sight of you would rekindle that part of his memory."

     They hoped it wouldn't as the pede steps of the titan entered the hangar from outside, rubbing his helm. His pinched expression made him look fierce, and angry, but the dent in his helm he had refused to allow Ratchet to fix revealed he was only annoyed by the sudden pain.

         "Ratchet, I'm afraid you were right about this blow. It-" He caught sight of the three human adolescence, raising an optic brow. "These are the three consultants you spoke of? They are much smaller than I had believed." His servo fell to his side slowly, seeing their fear, especially from the smallest of the three.

     Optimus sighed, but nodded.

         "Megatronus, this is Jackson Darby, Miko Nakadai and Rafael Esquival, the three human children we have allied with."

     Said adolescence jumped back when the silver mech kneeled with a surprisingly warming smile. He didn't seem all that fierce when his expression was so genuine.

         "No need to be so frightened," he greeted, "As Orion said, I am Megatronus, Gladiator of Kaon. I may look fierce, but Orion can tell you, friends of mine come to no harm." He offered a servo for them to shake, Jack being the bravest and shaking one of his pointed, scarred digits.

         "Jack Darby," the boy greeted in return.

     Raf was not so willing to befriend the war lord as quickly as Miko did. Jack was still wary, but the two held a strange understanding of each other. Megatronus held no sign of gaining his memory back, even as he came in with Miko in his palm. The girl was grinning madly, practically jumping in the once-enemy's servo. 

         "That, was awesome!" She cheered, "Jack you should have come with us! Megatronus can do a barrel roll quicker than even the jets here."

         "Your human technology is nowhere near as impressive as Cybertronian engineering." Megatronus chuckled, still holding the girl. "My form was built more for stability, however. I'm surprised you do not have fliers yourself, Orion. Has this war really taken such a toll on your ranks?"

     The Prime frowned still staring at the screens. The Decepticons had been looking tirelessly for their master since his disappearance. It did not bode well for them. He had hoped telling Megatronus a little about the war would ease his curiosity, but it had not, clearly.

         "I am afraid so, old friend," he nodded solemnly, "They were destroyed on Cybertron before we could gather them for the exodus."

         "A shame," his lost friend nodded, "I am glad to be of service in this infectious war. To think such a small species must endure it's horrors you've described so far." He pat Miko's head, making the girl laugh as she held onto his digit as if they were monkey bars. "The last I remember is we were planning on visiting the council. What happened afterward? Did we even make it?"

         "Yes," Optimus frowned, looking to the floor, "but I'm afraid it did not go as planned. In a way, we were both betrayed."

     Jack frowned as he watched them from the platform, having joined the still rather intimidated Raf. He wanted to ask Optimus if they were giving away to much information, but with the war lord standing next to him it was difficult. Optimus was right, Megatron was smart even as Megatronus. His skill certainly did not leave him, nor his mental prowess. It wasn't hard to believe maybe their new found ally was simply faking his amnesia. Megatron refused to falter from his guise, however, and the scans Ratchet revealed showed he was indeed an amnesiac. For now, anyway.

         "Young Jack," Megatronus greeted as he placed Miko on the ground to join her guardian, "I have yet to examine the entirety of your base on foot, would you do me the honors?"

         "Uh, sorry," Jack's expression became deadpan, confusing the giant before him, "no can do. I have- I have work to do. Human stuff."

         "I see," the gladiator nodded slowly, an optic brow raised in interest, "then may I observe these human activities to better understand your race? There were many other species who would join the Gladiatorial ranks on Kaon. I'd have to say the most irritating would be the-"

         "We're not something to be observed," Jack snapped, turning away from the gladiator, "what, you think you'll gain information to better kill us?"

         "I did not claim-"

         "Oh, really?"

         "Jackson," Optimus interrupted the one sided argument, the oldest boy holding an expression of pure hatred, Raf scooting away from both him and the titan, who held a rather confused and hurt expression, "I believe you will need to work on these activities you have mentioned instead of antagonizing our guest."

     The boy huffed, leaving the doors of Hangar E. Miko and Raf ran after him, leaving Megatronus with Optimus. The others bots were elsewhere, Ratchet stepping into a tense atmosphere that made his circuits prickle. He watched as Megatron stared at the empty platform, servos ready to transform if their guest were to attack the Prime. The war lord looked up, staring at the wall with a forlorn and lost expression. 

         "Why does an entire species, hate me, Orion." He asked raspily. "I expected a human military force to be wary of titans amongst them, especially having battled against our kind before, as you've told me. But three human younglings? Orion, my friend, what are you not telling me?"

     Optimus peered to his friend, seeing the unshed lubricant and clenched fist of a mentally battle worn mech. He was fighting with himself on the inside because of the evidence around him. He understood he had done something, but what that was, Megatronus was always unsure. The gladiator had taken notice of the insignia emblazoned on his chassis, and understood it was not like the other's symbol that banded them together. He was out of place among who he believed should be his friends. 

         "Megatronus, I am deeply sorry-"

         "Do not apologize to me, I want an answer." Turning to face his friend, the silver mech glowered at the other. "Why is my affiliated symbol so different from those around me? Where are Soundwave, his Minicons. They were our allies, Orion, why are they not here fighting for this planet against these so-called Decepticons?"

     Megatronus only needed his friend's refusal to look him in the optic to answer his questions, the mech standing straight, only to nearly fall back as his optics widened. He gripped the railing, making it bend and snap in his grip. He held his helm, wincing but refused Ratchet's help when he offered.

         "They're the Decepticons. I am a Decepticon. Orion who leads them, if that even is your designation anymore."

         "Megatronus, please, sit down-" Ratchet pleaded, but the menace merely pushed him away again.

         "Tell me!" But Optimus' silence told him more than enough. "How could you keep this from me so easily? We were brothers, we learned from each other, there were no secrets before. Why are there secrets now? Orion how could I possibly become a monster?"

     The just and humble leader closed his optics tightly, refusing to let his own lubricant leak out into the open. He did not wish to have this conversation. He only wanted his brother back, but it did not seem that it was meant to be. The Prime looked to the computer and brought up Megatron's file, his criminal record, and rank among the Decepticons. His friend brushed past Ratchet, despite his protests, and absorbed every bit of horrifying information.

         "Dark energon-" he breathed, "I nearly murdered Bumblebee and his charge?"

         "There have been many times when you have had the chance to murder us all, Megatronus." Optimus' frown deepened. "During the council meeting, you spoke of revolting, a complete upturn of the caste system by force. I tried to sway the council's original decision by speaking of peaceful ways to properly change Cybertron for it's betterment. They chose to elect me as the next Prime. Optimus Prime."

     Megatronus flung himself away from the terminal and the Autobot leader as if he had been stabbed, holding his pained processor. Half of him said his closest friend was only trying to help him, the other said he had been betrayed. Which was he to believe? To believe he had been betrayed would lead to chaos and further war. To believe Orion, no, Optimus had only been trying to help during that meeting would lead to who knows how many more secrets. If Optimus Prime had kept the gladiator's evil doings secret, what else would he hide? But the children- the humans. Sweet, little adventurous Miko. She had warmed up to him so readily. This species was so young and vulnerable. They had yet to experience deep space and its beauties.

     Straightening up to his full height, Megatronus stepped to the edge of the hangar, staring at a few jets that flew by in their usual flight patterns. The sun shown on their barely strong enough metal. They would so easily be shot down. The thought both exhilarated and frightened the mech, such memories beginning to surface as he thought more about being a monster. He vaguely remembered roaming the halls of the Nemesis war ship. Ghosts of orders flew past his hearing and a haunting war cry felt like it could burst from his vocals as his knees buckled. He felt the arms of Optimus hold him upright, and the Autobot medic scan him.

         "He's remembering," came the fearful realization.

         "Yes, I am." Megatronus muttered dryly. "I called myself Megatron. I slaughtered others left and right. Yet you did not think I needed to know this?" He hissed, peering at Optimus from the corner of his livid optic. "Optimus Prime indeed, you are nothing like the Orion Pax I had known!"

     He ripped himself from Optimus' hold, stumbling forward and having to hold his helm in a vain attempt to ease the stabbing pain of remembrance. He spotted the human Jack at the corner of his optic, the boy being followed by Rafael and soon Miko appeared. She gasped, tiny little hands coming up to her mouth in worry. She went to run toward the feared leader, but Jack stopped her.

         "I became a harbinger of death," Megatronus whimpered, dragging his servos down his helm, "And you believed I would return to that."

         "We did not know what to believe." Optimus told him. "Megatronus, come back inside, please."

     The mech stood, staring at the horizon before shaking his helm.

         "I will not. I do not belong to your team, but remembering my original cause-" Megatronus stared at his servos. They had shed so much innocent energon. That was not his plan, that was not his goal. His goal was to free others from the caste system, and instead he continued that system in his own ranks and even brought it to an innocent planet. "My memory was lost but for a little time, and the monster I had become is what I despised then. I am unsure of what I should do."

         "Come with us to fight." Optimus stepped forward, but Megatronus shook his helm, waving him away.

         "I will not fight alongside a faction meant to destroy me. But, to comfort those who have befriended me despite my crimes," he looked to Miko, who froze under his gaze, "I will not side with a faction so far from my original ideals."

     The girl ran to him, refusing to heed Jack's protests and hugged the giant's pede. Megatronus rested a large servo over her back before turning her around and sending her back to Optimus and Ratchet. He watched her tear up, smiling softly before looking to Optimus again.

         "You are not Orion Pax, and I can not be Megatron, nor Megatronus. My cause was lost eons ago. If you need me, call for D-16."

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You may all cry now.   >:)