The plan had been for Trunks to wait for Fluttershy's forces to be in place before he engaged Chrysalis atop Canterlot castle. Trunks didn't follow the plan.
With only Starlight by his side, Trunks flew straight to the main castle and landed in front of over a hundred changeling guards. The guards let out yelps of surprise as the swordsman landed in front of them, but that shock only lasted a moment before they drew their weapons and all lunged towards Trunks.
"Fluttershy told us to wait for her forces," Starlight reminded Trunks as he engaged the changelings.
"This way is faster," Trunks replied, dodging and blocking the spears and blades like they meant nothing to him. Which they did. He struck a changeling in the chest with his palm and rocketed the bug being out of the city. He swung around and threw a kick that caught a changeling in the head. That changelings headless body hit the ground a moment later.
"But aren't you supposed to only be focusing on Chrysalis? Why waste time fighting all of these...foot soldiers?" Starlight asked from behind a barrier of magic, blocking out the changelings that were trying to get to her.
"Because I'm hoping that the sight of a single being mopping up her forces, the big bad boss herself will come out to challenge me personally instead of trying to flee from the city of an army knocking at her doorstep," Trunks answered, before slamming his fist through another pair of changelings. Ki erupted from his arms and turned them to ash, before he spun around and fired numerous more ki blasts into the forces around him. They quickly joined the ash pile, leaving Trunks alone with Starlight a moment later.
"Geez, there were over a hundred of them and you did this to them in a matter of moments," Starlight said with a slightly nauseous look on her face. "Did you have to...slaughter them like this? I mean, they couldn't have all been evil, right?"
"Pretty soon this timeline won't exist. How I deal with them won't matter then," Trunks replied coldly. He then lifted his head to the sky as he sensed a stronger ki approaching, his eyes narrowing when he spied a changeling that was twice the size of all of the other ones descending down towards them with another army of changelings flanking her. Starlight moved closer to Trunks while the hero grabbed the hilt of his sword.
"Well I had to admit that this is a first," Chrysalis said with a laugh. "I cannot remember the last time that somepony came to me to die. Normally all those that oppose me hide out in that little forest and hope that I don't find them. But you came right to me. That eager to die, eh?"
"It doesn't matter what I say to you. In a matter of moments you'll be dead," Trunks replied as he drew his blade.
"Brave words. But can your skills back up your bravado?" Chrysalis asked before she signaled for her forces to descend. The changelings surrounding her all let out bellows of rage before they dive bombed Trunks, who stretched his neck slightly in reply.
The first changeling that reached him never even knew that it had been cut in half. It was dead before it hit the ground. The second, third and forth had just a moment to realize what had happened to their ally before they joined him as a pile of pieces on the ground. The changelings that had hurled themselves at Trunks realized that diving head first at the sword wielding saiyan was a pretty big mistake and ceased their charge.
"Not coming to me, eh? Fine, I'll join you up there." The words were barely out of Trunk's mouth before he appeared in the center of the horde. Some changelings barely had time to cry out before flashes of metal slashed across the sky, severing the changelings ties to the word of the living. Some of them managed to get off a few blasts of magic at Trunks, but he easily deflected them with his blade. A few more swings of his blade finished off the remaining changelings, leaving him as the only being flying in the sky.
"Alright Chrysalis, now that I've warmed up, what do you say we finish this?" Trunks asked as he looked around, only to find that the changeling queen was gone. He then glanced towards the ground and found that there were now two Starlight's standing side by side, with both of them looking up at him with shock and disbelief.
"Trunks! Chrysalis shape shifted herself into me! You need to stop her before she gets away!" one of the Starlight's yelled at him.
"Don't listen to her, she's the fake!" the other one yelled up to him. "Cut her down before she thinks of some trick to-"
Trunks lifted his arm and fired a blast of ki that caught the second Starlight in the chest, rocketing her backwards and sending her crashing through a brick wall. That Starlight hit the ground and gasped in pain, before she changed back into the queen of the changelings. "But...how...?"
"You changeling's all have different ki than the ponies. Even if you can shape shift in a way that makes me unalbe to tell you apart physically, I can tell which one's the fake by sensing your energies," Trunks replied coldly as he floated in front of Chrysalis, extending a hand towards her. "This ends here. You and this fractured timeline."
Chrysalis let out a bellow as she fired a blast of concentrated magic at Trunks. Trunks swatted away her strongest spell with the back of his hand before he returned fire with a blast of pure ki that consumed Chrysalis. She had just enough time to let out one last screech before she was turned to ash. "And that's that."
"So, what happens now?" Starlight asked, walking over to Trunks once he had touched down. Trunks turned to look at her, before glancing up to see that the sky had turned black. He then glanced back at Canterlot castle to see that the castle had vanished into the darkness as well. The rest of the world quickly followed suit, until the only beings that Trunks could see was himself and Starlight.
"This happens. This is what happened after I killed Sombra, so I assumed that something similar would happen once I took care of Chrysalis as well," Trunks replied, sheathing his sword. "Now the question is did our actions gain us the attention of Clockwork and Maestro like it did last time? Or are we just going to wake up in another timeline?"
"Hey Trunks...are you sure this is the right way to do this?" Starlight asked, turning Trunks attention to her. "I mean, erasing these timelines. I know you say that they're not real and just broken off parts of the main one, but..."
"Trunks me, this is for the best."
"Well I would have to disagree with that."
Trunks spun and fired a blast of ki towards the voice, but just like the last time he had tried to obliterate the metal being, the ki blast came to a halt right in front of Clockwork, suspended in time before it could strike him. "And I see that your manners are just as nonexistent as they were the last time we met. Hello again, Trunks. I am surprised to see you alive."
"Well don't be too surprised if you're not alive much longer," Trunks replied as he drew his blade and lunged towards Clockwork, closing the distance between the two faster than Starlight could process. Trunks blade flashed in the darkness and by the time Starlight's brain had caught up with what had happened, Clockwork was a pile of scrap at the feet of Trunks. Trunks narrowed his eyes at what had been Clockwork before he sheathed his blade and turned away.
"Can we please stop with this?"
Trunks eyes went wide as he spun around to see Clockwork standing behind Trunks, no sign of the damage upon his form that he had just suffered moments ago. The confusion and disbelief was clearly written on Trunks face and Clockwork was kind enough to explain what had happened.
"Maestro and I exist outside of time, Trunks. Strike me down, burn me alive, incinerate me...none of that means anything to me. But I ask that you please stop trying. It gets annoying have to rewind myself repeatedly to return to this form. I am rather fond of it. I believe it's the mustache."
"I'll strike you down as many times as I have to so long as it makes the main timeline safe," Trunks snarled in reply as he reached for his blade once more. This time, before he could grab it, Clockwork snapped his fingers and Trunks grabbed at nothing but air a moment later. He glanced over his shoulder to find that his blade was gone, and when he looked over at Clockwork he found that the metal being now held his blade.
"Trunks, there is nothing more annoying than being stuck on repeat. So how about we fast forward through the part where we fight and get to the part where you realize it's pointless and instead listen to what I have to say?" Clockwork offered, dangling Trunk's sword before him as he did so. Trunks narrowed his eyes, but didn't say anything, leaving an opening for Starlight to step forward.
"Excuse me, Mr. Clockwork?" Starlight asked, turning both sets of eyes towards her. "If you don't mind me asking, why are you tearing apart space and time for Equestria? Why have you fractured the timeline and made it so all these impossibilities have become possible?"
"Ah, finally, some pony with manners," Clockwork said, tossing the sword to the side before bowing to Starlight. "Greeting, Ms. Starlight. I am, as you said, Clockwork. Apprentice to the Maestro and currently the one tearing apart Equestria's timeline. I apologize for this, but there is no other way to achieve what I seek to achieve."
"And what is it that you seek to achieve?" Starlight asked, noticing that Trunks was charging up something in the palm of his hand.
"I am looking for something. A moment in my life that I cannot remember," Clockwork replied, reaching up and adjusting his hour hand part of his mustache. "A moment that forced me to become this-"
"MASENKO!" Trunks roared before he clasped both hands together over his hand, before thrusting both hands towards Clockwork and unleashing a hellish blast of yellow energy towards the being. Clockwork was consumed instantly by the blast and was rapidly burned away until there was nothing left, leaving a stunned Starlight and a smirking Trunks looking at the spot where he had been standing.
"Trunks, I was trying to find out what his backstory was!" Starlight said to Trunks.
"Doesn't matter now. He's gone, which means that we can focus solely on Maestro now and-"
"You really have trouble listening, don't you?" Trunks and Starlight spun around to see Clockwork standing behind, looking exactly like he did moments ago. "You cannot destroy me, Trunks. I exist outside of time. Destroying my body does nothing to me. Except get me sightly miffed."
Trunks dashed to his blade and drew it, but when he turned around he found Clockwork standing before him. "But since you seem so eager for battle, perhaps you would be more inclined to talk if you first let off some of that steam. Fortuntely for you, I know just the foe for you to face."
Trunks had barely moved towards Clockwork before both he and Starlight vanished, leaving the metal man alone with the sounds of his body ticking to keep him company.
"Yes, let us see if this strength of yours is really up to the test...oh darn, I forgot to thank him for helping me to narrow down my search," Clockwork said with a sigh before he brought up a map of the timelines, marking off another that was gone and noting that the main timeline was faded even further. "How do these eternal beings keep track of everything? No matter, let us see what Trunks can learn in this next world? I look forward to the fireworks."