Upon reaching the coordinates in question, the trio discovered that the Dayni Moon was an agricultural outpost, with diverse crops and strange looking sheep tended by robotic farmers. "A rather peaceful world," Clank commented.
"Should be easy enough to find Luna, then," Twilight growled, her wrench spinning idly in her magic. Ratchet echoed her sentiment by bringing the head of his wrench down in his hand a few times.
Shortly thereafter, they came across their first would be opponent, a robot with a rocket launcher. As they were walking down a narrow path with sheer cliffs to either side that disappeared into either clouds or fog below, Twilight seized the bot in her telekinesis and tossed it over the side.
When the sun went down, the sheep changed, becoming more monstrous in appearance. While Ratchet and Clank prepared to fight, Twilight smiled, charging a spell. When she zapped the sheep with the spell, they reverted to normal. "What was that?" Clank asked curiously.
"I recognized the transformation as an overproduction of monsterproposene in their brains, the same thing that affected Mr. ...the Proto-Pet," she explained, her voice trailing off towards the end. "I used the same spell to rebalance the production of that neuro-chemical in the sheep, since their gland is overstimulated by moonlight."
"Clever!" Ratchet praised, leading the way forward.
After leaping up a few replanted flowers to clear a cliff, the Luna-bot came into view, manipulating a few levers to send more monster sheep their way. Twilight de-monsterfied the sheep rapidly before seizing the Luna-bot in her telekinesis, dragging it forward. "I hope you didn't think you'd get away that easy!" she snapped, slamming the robo-ship into the nearby stone cliff face several times with mental force, following up by smashing it to bits with her wrench. After a great deal of smashing, the bot shut down, falling to pieces as the Technomites inside escaped. At the end, Twilight sighed happily. "...that felt good."
Ratchet and Clank stared in shock. "Well...that was...brutal."
"I hope there's enough left to scan for information," Clank pointed out.
"Oh, don't worry about that," Twilight countered, ripping a chunk of tech from the destroyed robot. "The nav comp's still intact, but any security systems are non-functional at this point. You can pluck their coordinates straight from it."
"You do try to think of everything, don't you?" Clank chuckled as he proceeded to scan the comp unit. "...their next destination was a Technomite manufacture facility...on Quodrona. I have the coordinates."
"Then we're done here," Ratchet confirmed. "Let's go."
As they landed on planet Quodrona, they once more found nothing of any interest that they could see. "Another dead end?" Ratchet asked morosely.
"No," Clank pointed out, picking up another miniature vehicle. "Another tiny facility."
"Then let's shrink down tiny, find the place, then expand back to normal and stomp the place flat!" Ratchet growled, punching his fist into his hand.
"Wouldn't work," Twilight pointed out. "Technomite metals can handle impact forces many times normal levels once shrunk, in much the same way an ant can lift so many times its own weight. The smaller you are, the tougher you are."
"Then I guess we'll take them out from the inside," Ratchet relented.
Once shrunk down, the three made their way to the Technomite facility. Once inside, they were confronted by turrets...backed up by clones of Ratchet. When Twilight saw the first copy of Ratchet shooting at her, she started to hyperventilate.
"Close your eyes," Ratchet ordered Twilight before blasting the clone to bits.
After that, Clank made a quick modification to Twilight's helmet. "There," he stated as a visor slipped over her eyes. "We and those we know well are marked as friendly targets in your sight now. You won't be able to see the shape of hostile targets, so you should be okay."
Twilight nodded in agreement, priming her weapons.
The path through the facility was quite straight forward, and beyond that point they were only assaulted by Ratchet clones. No longer able to see their shape - and the fact they were all mute - Twilight was able to fight against them more readily, though she seemed to get more and more disturbed as they moved forward. However, she refused to return to the ship, despite frequent suggestions that she should.
Eventually, the three encountered the leader of the Technomites and the mastermind behind their actions...Emperor Otto. He was a tall(1), thin, pale blue skinned being with a bulbous head, thinning black hair, a mustache, and a goatee. Twilight was privately of the opinion he couldn't look more evil if he tried, sitting there on his floating throne thing.
"Ratchet, how very nice to see you," Otto purred, his voice silky smooth. "Although I'm sure you've seen enough of yourself already." He began to laugh madly.
"So, what's this all about?' Twilight demanded. "Why clone Daddy? And...and why torture me like that?"
"Simply put, because you two are the most powerful heroes the galaxy has ever known," Otto explained. "An army of clones of the two of you would have been unstoppable in gathering the geniuses of the galaxy here to allow me to absorb their intelligence, thus gaining the most powerful mind the galaxy has ever seen!"
"It won't work," Twilight pointed out bluntly.
"Oh, what do you know?" Otto countered. "You're just a child! You couldn't possibly understand my-"
"An organic brain cannot handle a knowledge transfer," Twilight explained. "Even if you could develop a machine to transfer intelligence and brain power as data, an organic brain's capacity to store data is finite. Any transfer would overwrite a portion of the existing brain, meaning you'd lose some of your brain power with every transfer. Even if you could design a system that would add brain energy without overwriting, you'd also be gaining the personality data of the sophont being scanned, and you'd end up having a split persona of every sophont you copied into you. An advanced enough robotic brain might be able to handle the influx of data without crumbling, but it wouldn't be able to utilize the raw brain power as a telekinetic force as these blueprints indicate you intend."
Emperor Otto stared at her, completely flummoxed. "...how did you get a hold of my blueprints?" he demanded.
"A friend of mine sent me them," she explained. "And I was right, the fault in your design is the limitations of an organic brain. It wouldn't transfer the intelligence of the sophont in the left pod to the one in the right. It would overwrite the sophont in the right pod with a copy of the brain wave patterns of the sophont in the left pod."
"But...but that's impossible!" Otto proclaimed angrily. "My technology is perfect!"
"Oh, it is," Twilight chided. "Your tech works exactly as you designed it. But you obviously have no idea how the brain works."
Otto growled angrily. "I should have ordered you terminated when your samples proved useless!"
"You..." an angry voice growled from above as Qwark stepped up, gigantic relative to everyone else as he was normal size. "I didn't want to believe it...I wanted to believe I'd found my family...but you did that to Twilight?"
Otto moved his hover chair back. "Now son...I understand you're upset your little friend got hurt, but-" He was forced to leap sideways out of his chair as Qwark's fist crashed into it, flattening it to the ground.
"I thought you said Technomite stuff was tougher," Ratchet whispered as he staggered back from the impact and the buckling metal floor.
"Qwark doesn't know that," Twilight whispered back.
"What does that have to-"
"I analyzed his genetics," Twilight replied back quickly. "His brain chemistry is unique, and generates a reality weft centered around his person based in perception mechanics derived from certainty."
"What?" Ratchet asked, uncertain of the terms.
"He is physically capable of anything, as long as he has no reason to believe it is impossible," Clank translated.
"...his super power is ignorance?" Ratchet asked, groaning.
"And his weakness is fear," Clank finished.
As they staggered around, Qwark continued trying to crush Otto. "You're no father of mine! I knew that report was likely fake, but I wanted to give hope a chance! But you hurt Twilight!" He brought down both his clenched fists hard, sending towers tumbling. "For that you die!"
Scrambling, Otto managed to get a hold of the Shrink Ray Ratchet had dropped when he first lost his balance. Turning, he shrank Qwark down to the same size as everyone else.
"This changes nothing except how many times I have to hit you!" Qwark snarled, pounding his closed fist into his open hand.
"Oh, doesn't it?" Otto asked, smirking as he pointed the Shrink Ray at himself, causing himself to expand to what, relative to the others, was giant size, but was actually just their normal size.
Twilight smirked as she charged her horn, casting a spell on all four of them, returning them to normal size. "You didn't really think I'd spend that long with such a unique, energy based gadget without developing a spell form to do the same thing, did you?"
Otto grinned somewhat nervously. "How interesting," he began, lifting the Shrink Ray to his head.
Qwark's blaster snapped out from his holster, shooting the Shrink Ray out of Otto's hand. Before he could reach for it, Twilight had used her size manipulation spell to shrink him back down to his normal size, and trapped him under a force field.
"Well," Twilight began, walking forward to the small force field, smiling widely, "look how the tables have turned. It wasn't so long ago that you had me trapped, powerless in your clutches, helpless to resist against anything you might do to me." She lowered her head to look Otto in the eye as he flinched back from the electrical nature of his trap. "I imagine you expect me to show mercy, since I'm one of the heroes...but then again, on the other hand, you probably know how cruel children can be..."
She rose up over him, purple smoke pouring from the sides of her eyes. "So tell me, Otto...how does it feel to be completely helpless, and at the mercy of someone beyond your power to influence?" With a sudden movement, she brought her front hooves down hard on the shield, causing Otto to scream in pain inside as the electricity of the shield arced into and through him. "Tell me!" she roared, striking again. "How does it feel? How does it feel?" She struck again and again, her eyes going red as her coat started to darken.
She paused as her next hoof strike encountered metal rather than magic. Looking down, she saw Clank, his left arm buckling at the socket as his left hand held her hooves. He looked up at her, his eyes worried, compassionate...and pitying. "Not nearly as bad as it will feel for you...if I let you strike again."
Twilight blinked at him in confusion and anger...until she saw her own coat. Staring beyond him, she saw Otto, twitching and convulsing as the shield around him flickered. The next strike would have killed him. Twilight staggered back, her coloration returning to normal. "I didn't...I wouldn't...I...I didn't mean..."
Clank let his arm hang from its socket as he, Ratchet, and Qwark moved to embrace and comfort the poor filly, haunted by the darkness born of magic and pain.
(1) Relatively speaking, anyway. He was a Technomite, after all.