When Princess Celestia felt her sister return to Canterlot, she had a momentary swell of relief; she knew now at least where she was. That sense of things was quickly robbed of her when she then felt her sister move through the shadows in Canterlot to the Cathedral of the Elements. Whatever her reason for being there the situation had to be dire indeed, but there was nothing that she or her sister could do with them. In centuries past she had severed their link to the Elements so that neither she nor her sister could be tempted to abuse their power. Perhaps she had found Twilight and her friends? Whatever the case, she had to get down there quickly to see what was going on. With a bright golden flash the Princess of the Sun vanished, leaving behind two very confused bat pony guards at the doors of her Solarium. In the very moment that she materialized into the Cathedral, her sister was forcing her way into the mind of her eldest student.
Aghast, all she could say was, "What are you doing?!" So focused was she initially on the alarming invasion of Bunsen's mind that only then did she notice the presence of the others in the room: Bunsen's guards, the missing Lyra Heartstrings of all ponies, and two Ruined Ones, including- "You," she said with growing anger. She began to quickly stride towards him most of all, and almost on reflex her golden, wavy blade materialized at her right side, "What have you done to my sister, fiend? You've stolen her mind, haven't you?"
"Do not lay a hoof on him," Princess Luna blurted even as her eyes turned a vacant milky color, her horn just at the tip Bunsen's forehead, "My mind is my own, and he is more important than you know." Through memories years, even decades old she tumbled, looking for every scrap of evidence she could find of his wrongdoing. He had intentionally kidnapped Lyra and blamed it on Adam to get authoritative carte blanche on his pursuit. He had lied to both the Princesses about the human's measure of dangerousness. He-
The last thought seemed so ridiculous, so impossible, that she had to view it again and trace its origin back in his mind. He had been in charge of an emergency strike team that had been just outside Everfree Castle when the Elements had bound Nightmare Moon. She could see through his eyes the very outcropping he had hidden behind, remembered the cool night air escape his nostrils as they lay in wait. The soldiers near him were buckled up with war saddles, their guns ready to fire into the devastated castle. He had just loaded a round into his fellow's chamber; inside was a sickly orange liquid in a specialized glass round. The others didn't know for sure what it was, only that it was what could stop her if all else failed. This precaution was not sanctioned by the Princess; he had made this decision on his own, without her authority. The fluid, whatever it was, was the key to something darker.
"Luna, if you are truly in there I will find a way to free you," Princess Celestia said as she continued her march towards me, "After I've put this twisted being to rest, once and for all." She looked at me with a judgment of finality in her eyes, one like I'd never seen, and now I was afraid once again for my own existence; not for just my freedom, but now my life. "Adam, for what you've done, perverting the minds of my ponies, even twisting my sister's mind to your dark purpose, and for endangering all the world, there is only one place for you in all of existence."
Without giving any sign that she would have done so before she did it, Lyra took up a place directly in between me and the Princess. I blurted out in a panic, "Lyra, no! Don't-"
"Princess," she said as firmly as she could, even though she too was beginning to shake from fright, "Adam actually is better than you think: he never wanted to endanger anything or anypony, and he's trying to help save it all now."
The Princess' face remained firm, "Move aside child. I don't know if you are ensnared by him fully or if you made some pact with him, but he cannot offer you anything good. He's imprisoned you for too long, and your mind is bent around him, but you will be set free of him soon."
"I said lay not a hoof on him, Tia," Princess Luna yelled again, now more on edge than ever. The fluid was made down below in the bowels of the mountain, and tested on dark creatures. When at last it was finished he looked at the small sample of the first batch he had made. The Princess had assumed with her sister's return that there were only two options: eternal night or life without her. Now there was a third option: life without Nightmare Moon. "By the pits of Tartarus," she exclaimed softly, a thin vein of icy fear dripping into her voice.
"Princess," the Doctor now declared as he too came closer, "there is still time to set things right. We can close the Void hole with your help, but for the plan to work we need to be alive. If you can't see reason then I'll be forced to stop you. Please just listen to us and stop being so blasted stubborn for a second!"
The Princess' coronal mane began to glow even brighter, the edges of it flickering like the tip of a flame. Her blade began to waver slightly, and sparks of ether crackled off of it. "How dare you," she said angrily, and a white fire burned in her eyes, one that had not been seen for seven centuries, "I don't care about your deceit, manipulations or powers. I am the Avatar of the Sun. I am the Sun Unconquerable! By what right can you try to stop me in the defense of my world?"
An unnatural wind began to blow in through the open doors of the cathedral, ruffling the tapestries adorning the walls. The stained glass began to groan in their frames as a rapid pressure change took place, and they were trying to get out of the way of what was coming next. Lyra's mane and my shirt began to flap in the mysterious breeze, and we drew a little closer to each other. The Doctor's trenchcoat twisted and turned right along with us, but he didn’t seem to pay it any attention. A dark, angry frown had grown on his face, and he took step after step to confront the Princess, undaunted by her challenge.
Then, he answered it, "I am the last of my people; the last of the Time Lords.” As he approached her, his words seemed to carry a weight of their own, as if each was the heart of a black hole, “I am the Oncoming Storm." Everything in the room seemed to shrink and look pale before this man, as if he were the only constant, real thing, and that nothing else mattered, because all of existence, everything else known was trivial and in flux. “I have seen universes blossom in life and in their last spasms of death. I know of then, now, and all that is to come! You are the Unconquerable Sun? I am the Lord of Time Victorious! I am the Doctor! And no one stands in my way for long.”
“Is that a threat,” Princess Celestia spread her wings to their full span, and she did not give an inch of ground to his advance. The Doctor stood a mere three inches from her nose, both eyes glowed with ethereal energy. Hers were like the heart of a living sun, an inferno given life, burning bright as phosphorus. His eyes were like a field of stars; cauldrons of endless depth. These eyes had beheld everything that had ever existed, and were brimming with ancient but eternally young life. These were eyes like those of the ancient Greek gods, and they carried with them that same finality as what her words held. They both were unmatched, and now there seemed to be nothing standing in the way, leaving all the rest of us not as spectators, but collateral damage, “No, it’s a fact.”
“ENOUGH!!” Princess Luna finally roared as she disconnected from Bunsen Burner's consciousness and whirled around on the two of them. All became silent after the necessary outburst. With a heavy breath she looked back and forth between the two in frustration before speaking, “While we sit here posturing like quarrelsome foals, our world is nearing collapse! While Bunsen Burner has not known of it until recently, he has predominately used this as an opportunity to seize more power and to control both of us, even though we are mere hours from total annihilation!"
"Bunsen Burner has already proven his character to me," Princess Celestia said with a glance to her sister before returning her gaze to us, "and these Ruined continue to prove their own; overbearing, corrupt, and manipulative. Release my sister at once; this is your last warning."
"Bunsen Burner has been betraying your trust for years now," her sister said furiously, now fed up with her sister's stubbornness as well, "I have seen into his innermost thoughts! He went behind your back when Nightmare Moon returned. If Twilight failed he meant to kill me, and he even made the means to do it! He's had the ability to slay us for over a decade, and he believes he could replace us as well!"
“Lies,” muttered Bunsen Burner groggily as he reached once again for his glasses lying nearby. “All lies. Princess, your sister has been psychically taken by the subject. She is trying to destroy everything you’ve created!”
“Will your lies have no end, blackguard," Princess Luna snapped as her fury now instantly turned to him. She seized him telekinetically by the joints in his armor, and brought his face near hers. Princess Luna’s eyes glowed white with power, “Bunsen Burner, from this day onward, thou art hereby stripped of thy title as a Prince of Equestria, and thou art thusly banished from this capital of Equestria, never to return to it for the term of your natural life." The power dissipated just long enough for her eyes to convey just how absolute her words were, "May your name become a byword and be a shame to those called by it!”
Before anyone else could respond, even Bunsen Burner himself, he disappeared in a vibrant purple and blue flash of light. Princess Celestia gazed in horror as the last remaining sparks of her sister's magic descended to the floor, fizzling away. Her one ally that she had been so certain of, her student that she failed once before she had now failed again. Now she was alone. Everypony she cared for had been taken away, either physically or mentally. As she focused on that feeling her mane's luminosity grew until it shone like some otherworldly fire, ready to consume anything in its path. With this new and terrible light came her deepest wrath.
"You may have taken my students away," she snarled, and then brought her up sword, golden sparks flying everywhere, ready to cut us down, "You will not have her any longer! You will not take my sister from me!"
A golden field of magic formed around Lyra, not of her own making, and she was shoved roughly out of the way. With a grunt she fell to the floor before immediately shouting, "Princess, no!"
The Doctor was closest to the insane ruler, and he had even less time to respond than I before a gigantic cleaver came down on us. Without thinking at all, I put my good hand on the Doctor's shoulder and threw him off balance out of the way to the right, in the exact opposite direction as Lyra. I wasn't thinking beyond the fact that I wanted to live, when with so far unseen power the Dominion Gauntlet surged with energy. Reflexively I brought it up to protect my head and chest, when a grey barrier formed just in front of me between my attacker and I. The golden blade came down, and struck against it with a slight resonating gong. It then swung away, reflecting off of it, leaving both the Princess and myself incredibly surprised. An idiotic grin formed on my face when I realized that I had done it, I had done magic! It was short-lived indeed when she overcame her initial shock and began to slam her sword down more forcibly on my shield. Cracks quickly spread throughout its surface, until on the last blow the shield shattered completely, forcing me backward. Stumbling, almost falling, I saw her looming just over me, ready to drive home the killing blow. It should have been all over for me, but as the blade came down, a gateway opened up just between us, and Princess Luna's form flew out. Her trajectory was set already, and with a loud, "No," she intercepted her sister's strike with her own body. The golden sword, still fully materialized, was ripped away from Celestia's mental grip, and traveled with her sister as she crashed to the floor near Lyra. Purple feathers fell through the air, and Princess Luna's form lay still.
All of us looked on in utter horror, especially Lyra and the guards, but no one was so utterly terrified about what had happened as was Princess Celestia. The blade now vanishing from her sister's form, she rushed to her side with a yell of, "Luna!" As she at last stood over her she saw the ugly wound. A deep gash had caught the Princess of the Night in her midsection. Still terrified of what may happen if I came too close to look, I stayed where I was, but I was perplexed by one very simple fact: for a wound that looked that grave there was no blood whatsoever.
"Please get up, Lulu," we all heard her say softly. She began to quietly weep, her voice cracking even as she spoke anew, "Why did you? I didn't mean for this to-" She stopped and took a ragged breath, "Please just get up. Don't leave me alone again, Lulu. I'm so sorry."
Without any sort of warning or sign, greenish-yellow particles flew off of Princess Luna's still form and began to attach to Princess Celestia's coat. The fallen alicorn's eyes opened and she began to slowly but surely rise. From out of the grievous looking wound silver particles of light emerged, drawing back together the flesh that had riven apart until the light vanished with a quick flash, and the wound was there no more; not even a scar left behind to show for it.
"Are you alright, Dusk," the Maiden's voice asked, bewildering the guards with where it truly came from.
"I am fine, mother," she said with a slight twinge of pain in her voice, "but what about my sister?"
"Leave her to me. I will help her see reason one way or another." She then projected her voice towards the three of us, "As for you, Dusk will help you get to wherever you need to go to help end this threat to existence."
"That would be be my ship," called out the Doctor, "I can help guide the sealing process, making it like it was never there. It's in the forest just above where you found us."
"Good," the Princess said curtly, before she drew back the veil of reality and opened a portal to the space between existence.
As we made our way to this new exit, Lyra looked up at me mystified, "How is it you can throw up a shield that powerful, but you can't even do a real fizzle of magic when we need you to?"
I shrugged my shoulders and sighed heavily, "At this point I don't know and I'm not sure I really care. I just want this to be done so we can get back to our lives together."
" 'Together', huh," she said with a smirk, "Making a few assumptions, are we?"
"Well," I stopped and then stammered out, "Well, I, uh-"
"Oh, forget it," she said with a smile, "If nothing else you'll need a real teacher. Let's just take things slow, okay?"
I nodded wordlessly. It was more like I nodded dumbly with the facial expression I was sure to be giving.
After the three of us had stepped through the gateway across space with the Elements in hand and horn, Princess Luna looked back to the highest ranking officer amongst the guards, "Until this crisis is resolved and a replacement for the Director's chair is found, I place you in charge of the Royal Science Division. Return to the facilities below and handle business as you usually would. I will be near Ponyville."
"Y-Yes Your Highness," she said, unsure if things were returning to normal or if a coup had just occurred, "Lieutenant Swiftfeet and his squad are already in the area hunting down either the anomaly or a Ruined encampment."
"Then I suppose we will see him soon," was her simple reply. Her peace made, she stepped through her portal and sealed it off behind her.
The now temporary Director of the RSD pointed to two of her fellows, "Keep watch on the Princess, but from a distance. Don't intervene in any way, just stand back and observe whatever she does."
"Yes, ma'am," the two said.
They moved into position a few feet away, while the other four left the cathedral completely, all the while Princess Celestia stood still as a stone, the Maiden's lights glowing on her barrel.