I'm somewhat new to the fandom but I know there's some sore spots over portrayals of Celestia and depicting her in a negative light. With that said, I would like story recommendations where Twilight and Celestia are on opposite sides of an ideological conflict or where the Mane6 end up fighting Celestia in a civil war or clash in some sort of final confrontation.

Preferably both sides would be somewhat gray morally and have good arguments, but if Twilight turns into a power hungry self righteous tyrant who wants to send the Canterlot nobility to the guillotines or turns on her friends that's fine too.

I would prefer setups that do not involve comic book reasons to get good guys to fight each other, such as: mind control, possession, evil clones, parallel dimensions, magical corruption, brainwashing, and so on. You can still list them, but please make a note if something like that is the main driver of motivation.

I would especially like a story where Twilight starts off as a loyal subject to the crown until she sees the effects of empire, maybe confronts Celestia about it, is rebuffed and told it's the requirements of stability and so on, then rebels. If she wins and takes over and starts to act just like Celestia did and has a moment of realization, or someone calls her out on her behavior, even better.

I'll also accept stories where there's no physical confrontation, if the story itself is good. But I'm a sucker for a well done climactic battle scene. Twilight coming up with an elaborate plan to take out Celestia could be quite entertaining, I think.

Thanks.

Well, there is a fan game in development called Shattered Kingdom where you can potentially do that. Just do a net search on it.

5535280
Try "Lines and Webs" and its sequel by Airstream.

Sooooo, something like this?

"Are ya really sure 'bout this Twilight? Ah mean...ah sure as sugar am all fer taken down Celestia after everythin' she's done. But ya'll are her student ain't ya? Ya said it yerself, she practically raised ya from a filly...This can't really be easy fer ya..." Applejack pointed out.

"I must agree Darling. While we truly do need you in this...is it something you can really do?" Rarity wondered, her face still carefully hidden. With most of her business being in Canterlot itself, she couldn't really afford to reveal her face in these meetings, nor her coat, thus the dusty brown cloak she wore.

"And theres um...Rainbow Dash too..." Fluttershy mumbled, hanging her head.

"Tch, loyal my right hoof! How could she take in Pinkie Pie like that?!" Applejack fumed.

"Calm yourself dear, its unbecoming of you to lose your temper. We'll set things straight, but first let us be sure all is in order." Rarity glanced over at Twilight, the unicorn having stayed silent through everything. With a sigh she finally spoke.

"It's true. Theres a large part of me that thinks this is a terrible idea, a part of me that feels that Rainbow is right and that all of you should be thrown in the dungeons to rot...But after seeing what your lives are like...what you deal with on a day to day basis just to survive...I know deep in my heart that NONE of this is right and it MUST be stopped. Even if it costs me everything, I refuse to abandon any of you."

"That means a lot t' us sugarcube, but ah hope ya don't mind if we're jus' a bit cautious 'round ya."

"I understand...you've all known Rainbow for far longer than you've known me...All I have is my word and hope." Twilight sighed.

"It will have to do dear. I fear I have to cut our meeting short. The guards will be doing their rounds and if I am not home they will suspect something." Rarity gave a smile before lighting her horn and vanishing. Twilight filled her own horn with magic, gathering the residue from the teleport and forming a simple summoning spell with it, calling forth a few quills and some parchment.

"What...? Applejack began.

"A teleport leaves behind a trail that any Rookie Guard can easily trace. Guardsponies are trained to track down any Prohibited Magic. So I took proof of a teleport and hid it by calling some of my supplies to cover her tracks. So if they come searching..."

"All they find is you an yer supplies...Ah'm sure she appreciates it. Ah s'pose ah should get goin' too. They'll have to look hard t' find me in th' orchard, but eventually they'll comb th' whole thing. Ya'll get home safe, ya hear?" Applejack gave them both a hug, peeking out of the tent before galloping off into the distance.

"I'll walk you home if you like Fluttershy." Twilight smiled. The pegasus gave a nod in return, Twilight folding up the tent in her magic and tucking it into her saddlebags. The two marched in relative silence, Fluttershy constantly glancing up and behind herself. Twilight was sure her shy friend had taken everything harder than any of them. She had grown up with Rainbow Dash, and Pinkie Pie had just become Fluttershy's marefriend, her door to the world, her first steps out of her own shadow. And just like that she was gone, leaving Fluttershy to flounce about in the darkness alone.

"Twilight...th-thank you..." Fluttershy stammered, hanging her head.

"Of course Fluttershy, I'm always happy to help...out..." Twilight froze as guards landed around them, pointing spears at them both. Rainbow marched through them, chuckling and shaking her head.

"I should've known it was you." Rainbow sighed. She glanced over at Fluttershy.

"Good work Shy, I'll put in a word with the Princess and we'll see about visitation rights." Rainbow nodded to the guards.

"W-Wait! Y-You said you'd set her free!" Fluttershy cried as the guards lunged for Twilight. The unicorn grit her teeth, teleporting back and widening her stance.

"She lied Fluttershy! This is what they do!" Twilight yelled, firing a bolt into the nearest guards chest.

"I did what I had to! For the good of Equestria!" Rainbow yelled back.

"Is that how you sleep at night Rainbow?! After betraying your friends and everything you stood for?! And what did you get in return? A shiny badge, a pretty desk? Wonderbolt Supreme?" Twilight taunted as she popped in and out of sight, bolts flying and paralyzing one guard after another. Twilight vanished once more, but this time she didn't reappear. Rainbow swore under her breath, looking in every direction, gasping as a bolt pelted her side, dropping her to the ground.

"I didn't want it to come to this Rainbow. When you can walk again, make sure you give Celestia this message." Twilight leaned down, her eyes alight with mana.

"Ponyville will no longer be fuel for the Nobles. True heroes of Equestria are on the rise and one day they will claim Canterlot." She flared her horn, surrounding Rainbow and her company in the glow of her magic, teleporting them outside of Ponyville. She panted heavily, her legs wobbling as she turned and began marching towards Whitetail woods.

"T-Twilight..."

"You were desperate Fluttershy...I understand. You didn't trust me, you trusted the friend you've known your entire life. As long as I'm the only one you betrayed, I don't care. But Rainbow is never going to give you back Pinkie Pie. If it hadn't been for Celestia interfering she would've killed her right then and there. Let the others know, I'll be in the shadows..." Twilight winced as she filled her horn with magic one last time, vanishing before Fluttershy's eyes.

Just something that came to mind.

I just walk away doesn't have a war (yet, but post canterlot wedding Twilight despises her mentor for using her and then abandoning her, Twilight joins trixie and sunset shimmer on dimension hopping. eventually they get a droid army. but not sure when they'll use it.
bide not sure if you'll like this one, it involves Celestia and Twilight though I can't say much without actually spoiling the story.
Backwards through the mirror this story features Twilight being accused of being a traitor.
One Crime at a time Twilight as a little filly is a victim of crime, and goes all light yagami on everypony eventually culminating in a fight with Celestia of whether it was right or not for her to take revenge.

sky pirates of equestria, the manesix become pirates

memento mori
the outer dark
these two are fucking dark, twilight becomes a dark mage the story is told from the mane six perspective.

on the wings of grace definitely a war fic between twilight and celestia though the image makes it look like possession twilight actually only went darkside and thinks she's doing right.
negotiations it's set post conversion bureau and the humans have won, now Twilight must negotiate with the humans
the forgotten and exiled Twilight Sparkle, faithful student, best friend, mother to a dragon, daughter, sister, hero.
Banished and forgotten.
The day of her brother's wedding Twilight tried to do everything in her power to get her friends and family to listen to her about the fake Cadence but with time running out and with her brother in danger along with the capital, Twilight took it in her own hooves if no pony was going to listen.
Now banished and 10 years later, Twilight has changed more than any of her former friends and family could ever think.
war of the five sequel to forgotten and exiled 17 years after the events of Forgotten and Exiled, Equestria has fallen to civil war. 3 Generals have broken away to form their own nations. With Winter and Cadences help, Can a remorseful Celestia save her nation? Or will she only destroy it? As the redeemable are not always so easily redeemed.

split second this is one of my favorite fics Twilight Sparkle broke time when she got her cutie mark. Now Twilight and Sparkle are sisters from another time. Twilight is hailed as the potentially greatest light magician of all time, and already has a reputation as a hero by the time she goes to Ponyville. This isn't her story, not primarily.
Sparkle is an orphan - her dark magic killed her parents. She lives with her brother in Canterlot's industrial sector because they can't afford anything better. She can't leave either. She's a natural dark mage; while Sparkle won't go mad like Sombra, her reputation is hardly any better. Worse, the law doesn't see her as a good pony.
split second an eternity divided the sequel to split second.

the mare who once lived on the moon steampunk equestria Celestia is antagonist Luna is love interest, it's an alternate telling of friendship is magic.
brave new worlds it's a weird take, the main protagonist is luna and basically Twilight is acting strange. it's cyberpunk
Homecoming as a filly twilight sparkle disappears, she returns different, deadly and out for revenge on the two sisters who failed her as a filly.