Untold stories of brotherly love
None of these would actually happen, so I will call them AU

• Leaders in Bayverse
Samuel James Witwicky couldn't believe it was over. They had thought so when the Allspark was destroyed, but it turned out that the magnificent Cybertronian artifact had survived – with him. Then, they had thought so when Optimus had defeated the Fallen and the sun harvester was destroyed, but soon the Autobots were betrayed by someone they had once looked up to. So how could it be over now? He walked closer to the facility where the remains of many of the defeated Decepticons had been towed into, and he could hear his Cybertronian friends discussing something in the night's quiet. He could identify the irritated but enthusiastic words of Ratchet and the calm wisdom of Optimus Prime. There was a third voice, sarcastic and majestic at the same time. It was oddly familiar, but he couldn't put a name to it. He couldn't make out more than a few words (truce, understand, Prime, and possibly faith and agreement) with what little that remained of his knowledge of Cybertronian language. At least he wasn't seeing cyberoglyphs anymore.
There was something that sounded awfully like an apology from Optimus Prime, and he could hear Ratchet's name mentioned. The medic immediately snarled back a line about faith, and the second half of the sentence possibly had something to do with humans. The mysterious third voice replied in a bitter and serious tone, he said something about fleshling allies and he didn't sound to be very amused.
Sam finally decided to knock on the door and peered inside. Ratchet was working on a seemingly defunct and visibly halved head of Megatron while Optimus was busy pretending to be doing something entirely unrelated. His right arm was still missing, as if he had something more important to work on ever since the battle.
„What's going on?" he asked.
„Sam" Optimus walked over to him, kneeled down so that their heads were at almost the same level „There is something I need to know. I have witnessed your species' capacity for heroism and courage, but tell me, Samuel: are humans capable to understand the concepts of peace, understanding and forgiveness?"
Suddenly it all made sense. Giant robots talking about truce. Ratchet working on what seemed to be the Decepticon leader's carcass, but Sam had seen Megatron in worse condition, yet not dead for long enough. The third voice that belonged to no Autobot. And Optimus's words, many years ago in Mission City, when Sam first heard him call Megatron brother.
Those clear blue optics were pleading for the answer to be yes. The young man gave Megatron one more look, realizing that most of the cranial damage had already been repaired when no human was watching. He turned back to the Autobot leader, looked into his battle-worn face. „I won't tell William. Or Epps. Or anyone who would ever ask. I promise."