I saw the black mass blanketing canterlot, any hope at targeting chrysalis would be nearly impossible to fufill, so I decided to head for the castle, it would be the most likely to contain the changeling queen.

Alarms blared and fires raged across the griffon main base, the changelings had taken over.

"SIR! WE'VE GOTTEN AS MANY AS WE CAN EVAC'D WE NEED TO LEAVE NOW!" the general simply stared out at the destruction and quietly followed to the escape chopper.

The heli lifted away and joined the rest heading away from the destruction in the wake of the betrayal, only 4 out of the original 12 helicopters escaped to the capitol of griffonia. The griffons declared the changelings the more prudent threat and dropped any dissagreement with equestria in favor of living for another day. The front lines had a drastically different paradigm, the soldiers almost immediately stopped fighting each other to make an attempt to fight the swarm and try to escape.

Meanwhile in ponyville, a bright orange glowing thing streaked across the sky, all simply watched as it dove straight into canterlot.

I slowed down a bit and checked the castle, my hud didnt show her, so I swung back around and shot outside, i landed on one of the pillars to spot around, I saw the bitch hovering above the city watching the destruction from indide a massive force field, in her grasp were cuccoons that contained all 5 princesses, and twilight's friends being forced to watch the horrendous acts being committed below. All of my rage and pent up emotions came loose and I felt my insides boil, I summoned my sword and found my giant 30 mm cannon in my room, then returned to the roof of canterlot where I aimed up and pulled the trigger until the mag ran dry, all 5 AP bullets deflected from the shields with barely any effort, I dumped 4 more mags with antimagic and HE rounds, the shield fizzled, I dropped the cannon aside and shot ag her like a living tank shell, screaming.

"Hello Bitches! Im BAAAAAAAAACK!!!!"

I hit her like a freight train and sent her reeling back, we hovered momentarily until she shot back, I used a modified shield spell to send the bolt back at her, and she promptly caught it and reabsorbed the magic.

"Oh....look who we have he-THWACK" I gave her a smack upside the head and kicked her down, she blasted me back and threw a few powerful punches and I caught them...with my face and body. I slashed her with my sword and she blocked with a magic shield, she roundhouse kicked me and sent me through a building. I slung a thin beam of magic slashing across the sky, chrysalis deflected and shot back, i dodged and felt a shockwave as the bolt vaporised a building across town.

Twilight Pov.

I watched in horror as nova and chrysalis duked it out above, I wished that I could stop this...

Celestia Pov,

I saw great explosions above the city, the power involved was insane, billions of thaums of magical energy being expended, both combatants circling around each other, throwing building leveling blasts all the while. The collected love of countless ponies fueling chrysalis and the explosive rage of Nova keeping the fight going strong. I flinched in the cuccoon when a massive shockwave from a smaller blast touched down across town.

Luna pov.

We saw nova unleash her rage, much as we had done over a millenia ago, her body was changing, as she passed I saw her body begin to shift from it's normal purples and blues, to a firey purple mane and a body of jet black which began to heat intil it reached incandecencd and her eyes glowed a bright orange, her body was now comparable to celestia in height, the strikes only increased in force and frequency.

I fired the blade from my sword, and watched it sail through the shield and graze chrysalis on the side, the blade flew back and reattached itself to the hilt, I clipped the sword to my back and sent another magic beam her direction. With the second I bought I formed up a hilt for a weapon in my hand, and used magic to create the large sword blade, I swung the massive magic weapon at her and hit another magic blade, we exchanged slashes like madmen and I slowly pushed her towards the outskirts of the city.

Then it hit me... Something was amiss, supposedly she had defeated celestia... Yet somehow I was going toe to toe without being completely wiped off the planet by her. I sent an earthshattering magical beam in her direction before flying out over the empty fields around the mountain, Chrysalis' ire had been directed at me, therefore keeping it away from the city, I kept duking it out with her before the real heavy hitting attacks reared their ugly heads.

I was violently punted into the dirt below by a massive explosion before me, I climbed from the burning crater and immediately dumped concentrated magic downrange, then I rose up again and continued the dogfight above, to my suprise, I had done some damage, not much, but enough to give me a tiny ember of hope that I would survive...or even win.

"What a foal...thinking that you can take on a creature that has defeated celestia! You overestimate yourself..."
Before I could speak, I saw a massive pink cloud erupt from the changelings blanketing the city and envelop chrysalis.....

"You thought I wouldn't have a backup plan this time? What a foal....shame too, you would have made an excellent drone."
Chrysalis was now glowing a sicly green around the extremities and was considerably larger and more...jagged looking

I shot first and hit a shield, then I charged my sword with my magic and watched the blade become enveloped by plasma, soon forming something similar to a lightsaber, and soon we were driven back into a frenzy of strikes, neither combatant being able to land a strike on the other, attacks became FAR more violent when chrysalis sent a Huge magical Blast my way and hit me at point blank.

Twilight Pov

I was nervous, but not about my own fate as much as Nova, and the rest of equestria, now....it was looking pretty bad, Chrysalis was sending out enough energy to almost saturate Nova's magical resistance, the blasts alone were still able to throw around Nova Like a toy to a foal. I could only hope that She would last long enough to let a few escape. I witnessed chrysalis unleash a massive spell on Nova, sending her shooting through a building...at that moment, my hopes of surviving this were dwindling...ponies were dying left, right, and center, and our mose effective weapon had just been punted through a building.
She shot back out of the rubble quickly, but it did little to spur my hopes, If she had been thrown away that easily, it wouldn't matter if she got back up a hundred times.

I decided to make a change of plan, any of the attacks I could use without killing civillians were ineffective, a rifle against a tank would be an effective comparison, so I shot myself towards the encased princesses and party, and freed as many as I could before making a mad dash back to fight chrysalis...hopefully they would take the point and get the hell outta dodge.

Celestia Pov

I felt a blade graze my side as I saw nova sloppily hack it open, she moved to Luna and Cadence before shooting nack into the sky to distract chrysalis, my magic had been drained before my cucooning, as had everyone elses. I decided that it would be best to round up as many ponies as possible and evacuate the city.

I vaporized the rest of the cucoons and everyone began to follow me at the gesture of a hand towards a large public emergency shelter. As soon as we rushed in I began explaining my best contingency plan to everyone inside.

"Attention Ponies..." at that the room changed from panicked screams to almost silent in an instant,"...The ongoing fight outside has gone out of control, and we must evecuate the city...everyone here will follow twilight into the subterranian levels and escape the city through an underground train tunnel leading through the whitetail woods and looping back, from there you will head to the nearest town of ponyville, cadence and shining armor will come along and provide directions and protection, Luna and I will search for any other survivors, Twilight...make sure to evacuate the lower levels as well....Now, Lets Go..."
Everypony immediately scrambled to action and filed down to the lower levels Via, a small tunnel built into an underground bunker beneath the building. My sister and I went out.
*****
2 hours later, train tracks leaving canterlot.

Our bunch was now back together, we had managed to save about 300 ponies, and were now walking along the torn up train tracks away from canterlot...My sister and I had donned our millenias old armor and weapons to defend the group... All were weary, and not even pinkie could bring their spirits up...it tore me apart to see my little ponies in such a way...I also mourned countless lives in the city, and the ones who had died heroes defending the group...above the massive city I saw a flash and watched as Nova was blasted from the mountain into the grassy plains several megahooves east of ponyville, a smoldering crater was left behind, Nova Didn't get back up...she had fought valiantly...I continued my silence as I simply watched the black smoke rising from the crater.

3 days later,

We had finally reached ponyville, Luna had retrieved the battred, but still breathing form of Nova from the crater, she was now nude and caked with charred earth, her sword was retrieved from the dirt nearby, it was stained with the blood of countless changelings...maybe even chrysalis herself...the the blade was still true...but it was apparent that it and it's wielder had been shoved to tartarus and back.

Author's Note

So begins a second story arc ( this is almost completely unedited, I just wanted to get it out there, so feel free to point out any mistakes, I also kinda want to change a few bits to make it work better.