An add-on of Orion Pax: Part 1. Without Optimus Prime, the Autobots are leaderless, or so they think. The Fallen is a good guy in this by the way.
...
"Being a Decepticon is a choice, Agent Fowler." Ratchet said. "One that I have a hard time believing that Optimus would make at any point in his life. Orion Pax may not currently be an Autobot up here," the medic tapped his helm. "But I must never stop believing he would cease being one in here." He rested a servo over his spark.
Agent Fowler contemplated this for a moment. "With Optimus currently running with the 'cons, the question still stands. Who's in charge?"
"Yeah, how can Team Prime still be Team Prime without a Prime." Miko cut in, ignoring Jack's attempt to hush her.
"By seniority alone, Optimus would not have command." Ratchet replied. "However, given our current situation, there is one that command would fall to automatically. Team Prime isn't without a Prime after all." He looked to the black mech beside him.
Megatronus shook his head. "I left that life behind a long time ago, Ratchet." He rumbled.
"But you cannot deny that is who you are." The medic countered.
The Ancient Prime merely shook his head again.
...
Later, once the children left with their guardians, Ratchet and Megatronus were left alone.
"You must lead us." Ratchet told him.
"Ratchet, I can't!" Megatronus cried. "The very weight of being a Prime unleashed a side of me I had hoped would never come about. I murdered my own sister because of it..."
Ratchet cut him off. "I know the stories." He growled.
"Then why choose me?!" Megatronus snarled, his optics flaring.
"Because you are our only hope!" Ratchet snapped.
Megatronus fell silent.
"You are a Prime, Megatronus Prime. The second born of the Original Thirteen. You should've been in command this whole time. Yet you chose to step down and allow Optimus to lead. That's not what the stories say you would do." Ratchet said.
"At one time, I would've leaped at the chance to lead, yes that is true." Megatronus admitted.
"I don't think you're afraid to lead, Megatronus. You know what I think?" Ratchet asked. "I think you're ashamed. Ashamed of your title, ashamed to even think about leading. About even wanting to lead. So you don't. You step down and let others take the burden for you."
"You're right Ratchet! I am ashamed and as well I should be!" Megatronus snarled.
"You're not the same bot that you were then. You and I both know it!" Ratchet cried.
"You know it. I don't know what will happen if I take command." Megatronus whimpered, unable to hide the fear that lit his orange optics.
Ratchet's blue-greens met his gaze as the medic tilted his helm back to look at the Prime. "Prime's are born to lead. You can." He whispered.
"And if this goes badly?" Megatronus asked.
"You think I would let that happen." Ratchet snorted. "I'm not afraid to challenge Optimus when he gets a stupid idea in his processor. What makes you think I'd be afraid to do the same to you?"
"Good point." Megatronus conceded.
"So, will you lead us?" Ratchet pressed.
Megatronus sighed, half in defeat, half in acceptance. "Only until we get Optimus back." He poked a finger at the medic's chest. "Not one kilk longer, is that understood?"
Ratchet was unable to hide his smile. "Yes Prime."
He thought he saw a hint of humor in Megatronus as the Prime rolled his eyes.