Twilight explained the situation to Celestia and Twilight's sword was once again taken up in defence of the empire. Both Viceroys were at a loss to explain to Parliament and the empire at large what exactly the situation was. The only information they had was that a clone army was in the works, and that they had the most effective camouflage in history. Rarity and Twilight had poured over the logs of the fleets and not one had detected their presence. The ship Rainbow had damaged the least was recovered and its cockpit repaired. When they activated it's camouflage it was nearly invisible to the naked eye, and was absolutely undetectable by ship's scanners.
The few corpses that were able to be recovered proved to all be Changelings. A sentient race of humanoid creatures that could moderately change their height, facial structure, flesh tone, and eye colour. Each of the bodies found showed the tell tale scars of being cloned on the quick. What was most striking however was that each had a device implanted in their brains that after a little tinkering was revealed to cause complete control of their functions. The biggest problem for Twilight was that the Changelings weren't a space faring race, much less one capable of reaching Terra
The only Changelings that ever left their homeworld were ones hired to do parlor tricks with their shape shifting. Someone else would've had to do this to them.
Celestia was distraught that her information network had absolutely no knowledge of any cloning operation, much less that they were able to get an entire fleet to Terra herself. She had once conquered the stars by the sword, now her enemies drew up their camp right in her own backyard. Cloning had been frowned upon before Celestia, and was outright forbidden in the constitution, yet apparently a whole network had been cloned, armed, and deployed completely under the radar. Literally.
After a long discussion it was decided not to enact a full mobilization, as they had no idea what they were up against. The reserves were stationed around Terra, and the Imperial bastions around the empire were put in a state of war readiness. Twilight felt a little awkward that the military budget had been slashed due to the outbreak of peace, but Celestia assured her that the tax revenues resulting from the economic boom had more than made up for the deficit.
Rarity and S.P.I.K.E. worked tirelessly on trying to crack the camouflage unit, but nothing they tried seemed to work. Pinkie Pie suggested the fleets just constantly send out explosives into Imperial space to break their camouflage. Rarity considered this and the fleets were ordered to fire a salvo into the void at randomized times, but no fleet was ever discovered. A surly Applejack had been recalled only halfway through her R&R. She made the three week journey in only eighteen days. Rainbow was overjoyed to see her best friend again, but the situation made their reunion less than enjoyable. She groaned at the knowledge of an enemy that she couldn't fight. As much as she had wanted a new war, this one failed to satisfy. What was worse is that with Rarity and S.P.I.K.E busy trying to crack the cloner's camouflage, they weren't finishing there new mech suit they designed, so it just sat there, not murdering the crap out of cloners.
Twilight, despite being furious at the treachery against her empire, had a secret joy at the distraction from her project. The Discord Serum was safely in an evidence locker and she could think of anything else while dealing with this crisis. Fortunately or unfortunately however the crisis seemed to stagnate the second it was discovered. Celestia's information network placed former Admiral Davenport as their number one most wanted, but despite six months of relentless search, and countless savants pouring over volumes of data he was simply nowhere to be found.
Twilight sat with her head in her hands, her long ethereal hair spilling through her fingers and trailing across the floor like a fog machine spilling out its vapors. Pinkie Pie had become more and more accustomed to this posture and knew it was better to leave Twilight alone in this mood, but seeing her just so distraught always broke Pinkie's heart. She just had to do something. She went to the suite's kitchen and prepared Twilight's favorite tea. She put it on the warped saucer that Twilight had begun to call the cowbell in her mind. Pinkie positively loved sneaking up on Twilight, but right now wasn't the time for it, so she used the warped saucer to announce her presence as she entered the suite's bedroom that they shared.
She set the tea down on the tea table, called so as they almost never drank coffee, and sat down beside Twilight on the bed. She said nothing for a very long moment. It was a trial just to get Pinkie to sit still on a good day, much less when the woman she loved was in such a state, but she simply waited for Twilight to be ready to talk. After what felt like hours she let her head gently rest on Twilight's shoulder. Again nothing was said. Finally Twilight wrapped a wing around Pinkie's shoulder and pulled her into a hug. Pinkie embraced her gently and pressed her cheek against Twilight's neck. She always loved the way her sparkly hair tickled her face when they got close.
Pinkie heard that Twilight had finally said something, and she kicked herself for missing it. She reluctantly broke the hug and said, "Hrmm?"
Pinkie saw that Twilight had been softly crying. She was surprised to see that her tears were not those of sadness, but rather of frustration. Her face showed teeth grinding anger at her impotence. "How?" Twilight repeated. "How am I supposed to protect an empire of two trillion people, when I can't find their enemy." She rose and her aura began to light up the room. "We've tried everything Pinkie! I even went to the Changeling's homeworld, and I couldn't find a single scrap of evidence to show their involvement. How can I see across a galaxy, but I can't see the threat to my own planet!"
She dropped heavily on to the bed and wept into her hands. Pinkie draped her long pink curls over Twilight's shoulders the way she liked. "I know Sparkly Warkly, I know." She sighed hard and pressed a cheek to her beloved's gently shaking shoulder. "Of all the times I knew exactly where to throw a grenade I don't seem to know where to throw one when it counts. I'm sorry love muffin."
Twilight's head popped off her hands and she ground her teeth. She leapt to her feet and teleported out of the room. Pinkie was left in ear ringing silence trying to blink the spots out of her eyes. Twilight reappeared and yelled. "Do ya do it on purpose?! Because. . . FUCK!" She disappeared again and Pinkie decided to put on some sunglasses. She was glad she did because Twilight once again teleported into the room. "How long have you known? Because I need to know. . . Shi~" and with that she was gone again. When she came back she growled in the tone Pinkie knew meant she was genuinely mad, but not AT Pinkie. "You know you frustrate the shit out of me sometimes right?" Pinkie nodded with her big goofy smile. Twilight's scream of frustration died as she for a fourth time exited the room.
Pinkie'd had enough of this gag, and pounced on Twilight when she reentered the room. She cooed in her perpetually cheery voice, "So we gonna do something stupid and dangerous out of desperation?"
Twilight glared daggers at Pinkie Pie. She knew better than to ask how she always knew, but it still pissed her off to no end. After a long moment of angry silence she burst out with a loud. "NO! . . . MAYBE!! . . . FUCK!!!"