While I was off trying to see what was going on back on Earth, Twilight sent herself and my Equestrian counterpart back to Canterlot, where the situation was quite perilous.
"You stay here, I have to find my friends." Twilight said to Alicorn Kronos, quickly going to Ponyville, trying to find the other element bearers. Even though the Elements of Harmony were destroyed, perhaps it might be possible to use their power to best Tirek. It does make sense, since Tirek doesn't have to worry about the power of time, so Friendship could work as a method to defeat Tirek.
"I still cannot believe that Celestia was evil this whole time. She taught me so much, but...she conquered Equestria with blood… I am so shocked. Am I going to get compromised, too? I mean, she taught me about friendship, but...could I do something bad?" Twilight thinks to herself, mortified that her teacher was a warmonger all along.
After a few minutes of dodging debris and explosions, she finally makes it to Ponyville, but not all of her friends are there. She only sees Rainbow Dash and Rarity.
"Umm, Twilight, you look, uh, different." Rainbow Dash says, a bit surprised at Twilight's new regal, godlike form.
Twilight laughs: "It's a long story. I was in space, and Celestia was evil, and Nathan killed her, and-."
Rarity is shocked: "Celestia was evil? That doesn't make any sense? I knew Nightmare Moon was a problem, but CELESTIA? What happened to her?" Rarity asks.
"Well, apparently she took over Equestria with blood and conquest 1000 years ago with her sister, and Luna wanted the power all to herself, so she banished Luna to the moon. To clean up her image, Celestia used her magic to make up a complex mythology about friendship to garner support for future generations, and over time people forgot about her conquering past." Twilight says, crying. "I trusted her, she taught me so much, and Nathan had to remove both alicorns from the timeline. Equestria has no ruler now…" Twilight says, with hurt in her soul.
Rainbow Dash is confused: "Hold on, Twilight. Are you saying that Celestia worked with the Foundation?" Dashie asks her friend, worried about the possible connections to Kronos' backstory, and how he could react.
"No, I don't think so, but Luna definitely did, and she made Kronos go back in time to prevent the omnitrix from ever existing. Now Tirek and Vilgax can take over, and Luna would have too, if the time guys didn't clean up after her." Twilight replies.
"So, how are we going to defeat Tirek and Vilgax, darlings?" Rarity asks, unsure of how to proceed.
"Well, even if Celestia was making shit up about the magic of friendship, I have seen the Elements of Harmony actually work, and they are quite powerful. It's worth a shot. Kronos is on Earth, dealing with stuff there right now, so it is up to us to deal with this existential threat." Twilight says, assuming a more regal voice than usual.
"Okay, but if we ARE using the Elements of Harmony, where's everyone else? It's just the three of us right now." Dashie says, as she flies off to find the three other Element bearers.
"Well, Pinkie Pie went on a time travel mission with Kronos, so she might be nearby, I think?" Twilight asks herself.
EARTH, NEW YORK CITY, PRESENT DAY
I quickly make my way back to my apartment, and I turn on the television. The news is covering the recent events that took place in Equestria:
"It seems that Celestia, the sovereign ruler of Equestria, was actually a warlord the entire time! According to eyewitness reports, her real name is Supernova, and she conquered the land with blood a millennium ago. Thankfully, the new leader of Equestria, Queen Twilight Sparkle, has gathered her comrades in arms to deal with the current geopolitical situation, as well as Tirek's return. It is unknown whether the portal to Earth will be breached, but DEA chairwoman Samantha Johnson, who you might remember as one of the first hybrids, has issued a statement calming the american public, reassuring them that the Hybrids will handle the situation if need be Queen Twilight Sparkle has ordered all US embassy personnel to shelter in place in Canterlot, for their own safety. This is Andy Issacson, CNN, Equestrian Embassy, Washington, DC"
Holy shit. Besides the current clusterfuck that is happening right now in Equestria, it seems that Equestria actually established solid relations with Earth. They are a UN member state, they have a US embassy, and more. Impressive.
Wait, I forgot something! My parents are still at the End of Time in my secret hideout. I have to go get them. I quickly open a portal to the End of Time, and find my parents cowering in fear, unused to the vast expanse of spacetime in front of them.
"Why didn't you just put on a movie or something?" I ask my parents, pointing to the awesome 95" 8K TV I have mounted on the very fabric of reality, as well as my huge leather sofa.
"We are scared of floating in the vacuum of space. How are we even able to breathe?" My mother asks, puzzled.
"Well, in the event that I have visitors to my secret hideout, the very universe accommodates to their needs, creating a simulation of Earth-level gravity and atmospheric pressure. I call it the "housewarming spell." Damn, that is a cringey name.
"Whatever, that purple horse friend of yours sent us here so we didn't get hurt, so I guess that is helpful. What are you going to do about the alien invasion, Nathan?" My father asks.
"Honestly, I am done with all of this hero shit. I killed the mare who made me a god, and Celestia turned out to be a genocidal maniac named Supernova. I just want to crash here, at the End of Time and put on a shounen anime or something. I need a break. Twilight is a very capable mare, and now that she got promoted to godhood, I think she can handle this shit on her own, with her Equestrian friends. Wouldn't you agree?" I ask rhetorically.
"What are you talking about? Didn't the purple horse save your life? How selfish are you!" My mother asks me, with tears down her face. "I know I didn't raise you or anything, but if I did, I wouldn't have raised a quitter!" My mother says, begging me to intervene.
"Did you not see that Celestial Sapien thing?" I ask, projecting the past events onto the cosmos itself, along with the Celestial Sapien Hybrid girl.
"Holy shit… It doesn't matter, go help your friends! Isn't that magical or something?" My father asks me.
Ah, dammit. I hate it when other people are probably right. I snap my fingers, returning all three of us to the present day, back in our Manhattan apartment.
"What...How...Nevermind." My mother says.
"Are you going to pick up that kid with the watch?" My father asks me.
"No, he got redirected in time, stupid Luna made me rewrite history. I will tell you more when I get back." I say as I return to Equestria, having dealt with all of the problems on Earth and at the End of Time.
PONYVILLE, EQUESTRIA: PRESENT DAY
While I was dealing with stuff on Earth, it seems that the newly deified Twilight reassembled the Elements of Harmony.
"Glad to see you got the group back together. If only The Beatles did that, too." I quip.
"Not funny, dingus." Dashie says to me, nudging me in the shoulder.
"Don't provoke me, Dashie." I warn her. She backs off.
"Okay, here's the plan. Even if the Elements themselves were destroyed, their spirits live within us. If our friendship really is strong, then Tirek will be defeated." Twilight says, putting her hoof in the middle of the group. The other ponies do the same, and they all begin to glow.
"Ah shit, this is gonna be cool." I think to myself as the six ponies get enveloped in the magic of friendship. Even if Supernova/Celestia was some crazy maniac, I bet she didn't think her mythology of friendship would actually work. I just hope it doesn't corrupt these ponies like it did for her.
"Tirek! Cease your carnage and face us!" Twilight says, quickly gaining Tirek's attention from his previous occupation of crushing ponies to death like ants.
"Why would I do that? You think I am any better than your rulers? They were just as nefarious as me. You are all misguided fools. I pity you, Equestrians. Vilgax is coming, and he will destroy you, if I don't do it first!" Tirek says, charging a massive blast of dark energy.
Rarity puts up a magic shield, and I fly out of the way to not get hit by the attack. The shield deflects the blast, enraging Tirek, who charges towards the ponies, with the goal of crushing them.
"Fat chance, sicko!" Dashie says, flying up towards the clouds and creating static electricity.
"Pegasi controls the weather, so I am going to give you some SHOCKING news!" Rainbow Dash says, sending a massive bolt of lightning towards Tirek, electrocuting him and leaving him in place for a few moments.
"Uh, Sugarcube, I don't think that is gonna work. You just pissed him off." Applejack comments. "Pinkie! You still got that cannon of yours?" Applejack asks her friend, who quickly runs off to her house, and rolls the cannon over to Applejack.
"Uh, what do you have for ammunition, AJ?" Pinkie asks, remembering my advice to stay in character and not repeat the time travel fiasco with Azimuth back in 1096.
"Well, I have apples, so that might not do much, but I think we can put some boulders in here or somethin'." Applejack says, quickly galloping off to find a few boulders. She found three large boulder, and pushed them over to the cannon.
"This could work." Pinkie Pie thinks to herself, as she loads the first boulder into the cannon.
"KRONOS. I NEED SOME FLAME TO IGNITE THE CANNON!. GET YOUR BUTT OVER HERE!" Pinkie Pie scream, inadvertently alerting Tirek of our plan to use the cannon.
"What do you think you are doing? Idiots!" Tirek says, blowing up the cannon with dark energy.
"Which one of you morons thought a cannon would harm me, the mighty Tirek!" he shouted, realizing that Pinkie Pie is the same color as the cannon.
"You have made a fatal mistake, fool. Prepare to die!" Tirek says, as he charges a massive blast of dark energy and fires it at Pinkie Pie, hitting her point blank.
"NO!!!" Applejack says, quickly running over to Pinkie's side, to make sure she is alive.
Oh shit. Not again. I don't like Pinkie, not one bit, but nobody should be killed like this.
The other ponies quickly run over to Pinkie Pie, and see that she is probably dying. I go over to the group, and analyze the situation.
"Uh, Nathan, can't you rewind time to save her?" Fluttershy asks, scared out of her mind that Tirek probably killed one of her friends.
What am I supposed to say? I mean, I COULD rewind time to save her, but death is an absolute point in time. I only got away with reviving my mother by resetting the universe, effectively making a new version of her.
"K...Kronos… I am sorry that I broke character back in the p..ast…" Pinkie Pie says as she falls limp. I check her pulse, and realize that she has left the mortal plane.
I feel horrible, even though I am not close with her. Pinkie is dead, and I didn't do enough to save her.
"You bastard!" Dashie says, launching herself back into the air, flying around in circles, trying to build up speed. It works, causing a Sonic Rainboom, which knocks Tirek onto the floor.
"Cease fighting, Equestrians!" Says an unknown voice.
I look behind me, and see a Celestial Sapien. Not just ANY Celestial Sapien, but one with a green mark on its chest.
"Ben??!?!" I think to myself. How? I rewrote history. This shouldn't be possible, but it's happening.
"Nathan, looks like your shapeshifting friend is back." Twilight says to me privately.
Indeed he is. It's hero time!