Please tell me X actually gets defeated in this story. I was always disappointed how Sonic and X were never able to fight in the video game adaptation, especially since it would've felt really good to see Sonic defeat X.

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Well, in the early stages of this story, I ordinally wanted Sonic.Exe to be the big bad, but I thought that would be too simple and to me it didn't really fit I mean, don't get me wrong I would like to see Sonic defeat Sonic.Exe but in the end, I scrapped the old draft in favor of Exelon who is my Exe OC character I made since I started getting into Sonic.Exe to be the big bad while Sonic.Exe would remain in the first chapter then be a major character in the other two chapters.

Since there wasn't a lot of Fanfics with Sonic.Exe in them, I thought I would write a story with an interesting plot

But to answer your question outright: X will fight Sonic and the Mane Six in the Third and Final Chapter of the trilogy after... well I won't spoil it

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And to add on my respond, if you like you can join my group and write a side story based off my Nightmares of Hell Trilogy

Not bad

NIGHTMARES OF HELL
Phase One: ACTs Forest/Caves and Castle

Phase Two: ACTs Orchard and Generosity

Phase Three: Rainbow Vs Exelon

Phase Four: ACTs Cupcakes and Magic Duel

Phase Five: ACTs Canterlot and Finale

Future: Nightmares of Hell: Round 2 will be in development soon, An MLP X Godzilla Crossover will be in development soon, and two Twilight focused fanfictions will be in development soon, for members of into the Ponyverse group I'll soon upload a news bulletin calling for suggestions on how to improve the betterment of our group's unity because I admit I can't do this alone.

This will be put on hiatus till further notice, the story is not cancelled only on pause

I'M BACK EVERBODY!

Will now continue this project, and just for you guys and girls a sneak peek of my lyrical song for the Finale Act: Harmonic Trouble
Red for Rainbow/Iris and Yellow for Fluttershy.

Drowning, Drowning
Sinking, Sinking
Darkness rising, Hope is Dying
Your world will soon be mine and
Your souls will soon be mine
FOR ALL ETERNITY

Can't Give in, won't give in
Must not fall, Will not fall
Beat the Darkness, Hope will rise
This world will be saved and
Your terror will end
FOR HARMONY ITSELF