“Well then,” Red says to herself. “I suppose I better see what you had to say, huh? Let’s see what sort of plan we need to make.”

Dlaf rferg
Red the badass? Is she gonna go full Rambo on Fluttershy? Possibly

Red looks down to her clothes. The gun. Her loyal companion.

“I guess I have changed… haven’t I? Have I changed too much? I really hope not. I’ve been thinking of him so much… trying to make sure that I can save him or help him. But what if I’m not what he wants anymore?”

Red closes her eyes and takes a deep breath.

“Then he’ll at least have his freedom.”

KobraNerd
i'd say sneak.

“I have to admit, that’s where I’m thinking too. If I sneak in under the cover of night, I might be able to pick off enough guards to get him completely out and never be noticed.”

Methmadod
EPIC BATTLE

Red nods, but then shakes her head.

“My big worry is that, all of these ponies here… they’re real. Maybe not physically. Maybe not even WE are physically real, but they’re real to some other pony here. Isn’t that worth protecting? I want to save lives. Not hurt even more. Then that makes me as bad as her.”

Winkdude
One shot one kill.

“But then again, I’m taking a life… Should I really kill Fluttershy?”

ThePanzerLover
Is there really ever an end? Whats the purpose of continuing? Why not just end everyone and everything? If it doesn't work she'll just resurrect it all and try again anyway.

Red sighs and lays down on the cot in her tent.
“I’ve been asking myself that too. I ask it every day. I have the tools. Right here. I could try.”

She closes her eyes.

“But I wanna believe that if I fight hard enough. If I do the right things, maybe I can put some sort of meaningful closure to all of this. If not for me… then.”

AgencyFB
There's only one way to deal with reality benders.
Do not try to reason with her.
Do not try to bargain with her.
And certainly do not spare her life. Kill her, by any means necessary. The stakes are too high. Anyone that dies in the crossfire is spared living the life of a hapless toy.
Fluttershy's too far gone. She doesn't feel pity, remorse, or fear. She's out there, she knows you're alive, and she absolutely will not stop coming after you until you are dead.
If the worst comes to pass, save the last three bullets for yourself, Anon, and Red.

Red closes her eyes and her loyal companion walks over and lays beside her.

“I know. I know all of these. I know you’re right. I know it’s what I need to do.”

She blinks and a tear runs down her face.

“I just wish there was another way.”

TwistedSpring
Yeah red I gotta agree. She’s too Dangerous while the system is in place. Something had to be done about flutters.

“It’s just… Killing somepony. It’s supposed to be so permanent. So… real. But she brought Anon back. She brought herself back. I still don’t get why I’m so special. Maybe it’s because of you. All of you. You gave me the powers to stay alive, even if I shouldn’t have. But her… there’s something else. And I don’t know if just killing her will stop it.”

“I don’t even know if I have it in me.”

Dustchu
Become Solid Snake

“I suppose all I can really do is make a plan and roll with it. Stealth seems to be the best option. But if I kill Fluttershy, then Alerts will freak if I don’t do it quickly and right the first time. If I save Anon but don’t kill Fluttershy… nothing changes.”

A_Mustang
Sneak into the camp, slit her throat and hold her down till she stops squirming.
This buys you time.
She will respawn, and from what it seems, she will remember. If that happens, the die is cast.
But while she is dead, an opportunity is presented. REWRITE HER. Return her to her base exisitance, erase her memories, and remold the story. Make her get over the crush she had when she realizes he's a real person. Fold her into the background and make your cuts clean.
And if that doesn't work, simply erase her.

Redheart sits up.

“Can… can I do that? How would I do that? I barely know what to do, how to do it now…”

Red sighed and folded her hooves.

“I wish the guide were able to help. He seemed to know the tools really well. Maybe he could have done it. I don’t know.”

Twilight_the_spy
Remember that even though you removed privileges, Anon will still have protections. You (and everything else) cannot hurt him. I dont have a plan myself, but you can use this information to help mould whatever plan you may be considering to help you get yourself and Anon out of there.

“That’s right. If I went in guns blazing, it could hurt Fluttershy, but not Anon. Or at least, he won’t die. That’s really important.”

Wydril
Overwhelming violence. No one can raise the alarm if everyone is dead.

“Well if it’s just so easy, why don’t you just kill everypony?”

Red sits and sighs, burying her head in her hooves.

“I’m sorry. I didn’t mean it Wydril. I just… It’s just so hard.”

Milos
Torture her for taking away your love. Make yourself ino an administator and rip reality apart from around Fluttershy. Make her suffer an eternity twice, so that her mind will break. Teach her the meaning of the word fear.
OOOORRRR, set the world right. Reset back to before Fluttershy found the command console and find it yourself, banning her from ever being able to pervert reality.

“If I can… I want to exactly that. The second half. If I can reset everything back to normal before all of… this then I will. Don’t doubt that for a second.”

“Even if that means… I don’t get my happy ending.”

Pogmin
I'll be honest, I'm still fairly confused as to what's going on, but I'd recommend maybe figuring out a way to contact Anon before any battle? If you could both coordinate some kind of plan against Fluttershy it'd be a lot easier.

“I assure you. I’ve tried. If I could, I would.”

Jeff0ry
Try the commands:
#ADD_PROTECTIONS &#%$^@
#ADD_PROTECTIONS Red
#REMOVE_PROTECTIONS Fluttershy
If these commands cannot be done from your terminal you won't be able to just straight up kill Fluttershy, she has the cards on her side of the table

“I just did. All protection commands are secured right now because all users are locked out. She doesn’t have control. So, I’d bet that both Fluttershy AND Anon can’t be killed. Maybe… that means neither can I. I don’t know.”

AMuffinlover
Not lose to Fluttershy

“If it’s the last thing I do, I refuse to lose to her.”

PVCmech
Make a chronjob Wͫͩ́͗̊h̅̆̽̽y ex̅͌̋͂c̿ͣ̑̽ͨ͑̈́ȗ͂ͬͥͫͥsͦ̉e̿ ̓͛̂̒mē̈ͬ̔̚,ͦ̇͆ͨͥ̅ ͑̌̊ͬ̓̚m̍ͬyͪ ͂̀ͣ͒ͯ͗͑f̉̂̒̚ŕ̏ͧï̑e͒n͐ͬ̂͗ͤͪd͌̀ͪͣ͗.ͣ̅̏ͦͧ ̇̐ͭ̎̔̒ͮI̋̀̚ ̾d̑͌ͩ͑oͬͫ͗ ͩ̏b̌̊̒̓̋e͐͆̋͂̂̚lͨ̊̚iͩ̿èvȅ̊̊̉̾ ̓̽̈́yͬ̓̆ͧ̒̉ou ̀̚m̆̀eͥͮͤ̐a͑ͫ̓͑ͤ̌̈n̋ͤ̓ ͭͦ͗̉̚ä͒̎͂͆ͮͤ ̈́ͦ̓͆̑cͧͣ̐ͫrͨͨͪ̓o͑̅͆nͥ͗ͫj͌͌̽̇͑͐ob̑ͣ.̿ͩ̀ͩ̚̚ ͋H͐̿͌̿ͧ̃̓o͋͌̍ͬ͆̋̓ẘ̃eͮͪͫ̓ͩ̂v̀̓͆e̋̏̎̏ͣͨr͗̍̓ͩ̑,̎͗̂̚ ̊͑ͩͬ̈́͐m̈ÿ̈́͆ͭ̔ͬ ̔ͩ̑̀̀̑ͬt̀ͧě̍ͩ̔͊ͮr̆̇̔ͦͫ͗mͯ͑i̐̒̇͑ń͑̅̓̄alͤͧ̅̈́̑ i͗̍͂ͦ̌ͣs̾ͯ̚n̅̏̇̌ͬ̊’̈́ͨ̾͋̋͂̏t́ͫ ͥ̊̌ͣͬ̈́d̋̆e͊ͬͬ̌̂s̃igͥ͛̑n̚e͐̀̈̓͐̿d̉̐͐͐ ͊͂̓̉ͯ͌̍t͛ŏ ͦͧ̓̽ͨ̈ǘ͊̅s̈́̾ͫ̒e͛̌̽̀̊ ͗̄̂ͥ͆̀̈́s̎͊ͥ̌̉o̾m̊e ̈͌̉͂̃ͤš́ͨ͛̂ͨͦo̒͐̑͊ͦrͦ͗̂̓̌t ̂o̎͑͆f̿̈́ͨͦ͂̒ͫ ̈̅͒͌t͛̿͛ͬyp͗ȋ̿̔c̔͗́̂ͦͥaͬ̈l ́ͨ̿͐̑ͬ̚Unͮ͐i̓xͪ́ ̚Sͫ̇͋ͦyṡ͆͒ͯͥ̾̈́t͂̇̊̾̈́̈́̚e̋͑ͬ̈́̂ͭṁ͐͐̆.̔͛͐ ͦ̆̾͗Bu̔͌tͭ̑̓͆̌ ͬ͋̒̏͂ͥ̏I̾̔̾̓̚̚ d̐͛̈́̋ŏ ͣappȑ͗e̔̊ͧ̽ͪc̃̂͌̓i͋aͭͭ̚te͂̓͛͆̔ͧ͐ ͂yͤ̋͂̓oͥ͑̒̏̃̔̅ŭ͑ͤrͪ̂̓̆ ̈́̎̂͛͗ȁ͋ͤ̎ͦ̾͂t͛̎tͮëͯm͑́̓̆pͭͧ͊̾ͥ̅t ͥt̿̒̄̈o ͤ̇ͫ͆ͤ̚aͬͧ̃b̆u̔͆͑̋͗͋̂s͛̋ͩ̀͋ẽ̾͂ͮ̎ͩ ͋̆͗̆͆͐m̒͑̆y̑̌̉̂̋̇̚ ͒̔̑̂s͐̉ͥͬͨ̐y̐ͮͦ̊͗̓̚sͮ̓t̿̐̀̊͛e͗͑mͦ͂ͮ̎ͨ.ͩ̿̃ͧ͒ -admin to reintroduce a backdoor, keylogger, maybe swap out binary executables for su or sudo, misconfigure sudoers, anything to keep persistence.

“Strange. This message is corrupted. I don’t think I got this one.”

TwistedSpring
Fluttershy dosent have protections. I would suggest a desert snake or scorpion but she’s Fluttershy. Offing her with a weapon has potential but don’t go in close. She’s wrestled bears. Try poison/ an “accident”/ archery. Or even just informing our human friend that she dosent have protection anymore and he can use his immortal ass to do it at no risk.

“Then… I think it’s settled. We go in under the cover of night and… with a little luck. We save Anon.”

“And… I’ll try to kill Fluttershy.”

“Wish me luck.”