I just got this idea of Fluttershy accidentally got caught in a teleportation spell whiched went wrong and transported her to Reach when the Pillar of Autumn was about to take off but during the teleportation, it altered her physical autonomey to a spartan's and returns to Equestria after the Ark destruction.

this will take place in the in Halo Reach (2nd last mission of the campaign), Halo CE, Halo 2 and 3

and her arsenal.

A Sniper Rifle System 99 Anti Materiel

BR55HB SR Battle rifle

MA5C Individual Combat System

M90 Close Assault Weapon System

M41 Surface-to-Surface Rocket Medium Anti-Vehicle/Assault Weapon

M392 Designated Marksman Rifle

M7/Caseless Submachine Gun

M6D_Personal_Defense_Weapon_System

Type-1 Energy Sword

Equipment:

MRE's

Type-3 Antipersonnel/Antimateriel Incendiary grenade

Type-2 Antipersonnel Fragmentation grenade

Type-1 Antipersonnel grenade

M9 High-Explosive Dual-Purpose grenade

Combat Knife

Her armor:

Mk V

Or

Mk VI

Armor: Mark V, but with some parts or upgrades from the Mark VI.

Start her in the Mk V, she can upgrade later to the Mk VI.

That said, two things I'd like to ask, first do you want to do this story solo or as part of something else because we're working up a group collab at the moment? Secondly how are you intending on making Fluttershy fight? Since even if she got transfigured into a Spartan II, she wouldn't necessarily have the killer instinct they do initially and some of that is due to the fact they've had around a decade of training to fall back on, Fluttershy doesn't.

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Group collab I don't know. But her killer instinct will be activate during the final days of Reach

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It's up to you, though if you're interested in information, you can find some here: Returning from the Storm

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May want to cut down on her arsenal a bit. In game, Spartans only carry two weapons (three while duel wielding), and in canon, I think they mostly make do with two, along with a knife, or possibly the energy sword.