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The Mane Six

Twilight Sparkle

Twilight Sparkle / Ancora

Armor-Piercing Response: After South tries to justify her murder of North, Twilight talks about how Luna had allowed her jealousy of her own sibling to turn her into a destructive tyrant, but ultimately came back from the brink.
South: Is there a point to this story?
Twilight: What I'm trying to say is… you're only a monster if you choose to be.
Birds of a Feather: She immediately bonds with Simmons out of their shared nerdiness.
Break the Cutie: Fragmentation really does a number on her.
Butt-Monkey: Nothing goes right for her the second she gets to Repertum.
The Corruptible: Played for Laughs. The Reds and Blues manage to make her as snarky as they are.
Deadpan Snarker: Her time with the Reds and Blues greatly enhances her snarkiness.
Mirror Character: For Church. They're both beleaguered but Not So Above It All straight men who deal with an insane group they call friends and they're both forms of artificial intelligence. They wind up bonding over it.
Tomato in the Mirror: She is revealed to be an MI created by Sunset Shimmer during her time with Project Freelancer as part of the Director's attempts to revive Allison.
Took a Level in Jerkass: Downplayed, but her time with the Reds and Blues makes her increasingly sardonic and acerbic.
Wide-Eyed Idealist: She starts off as this, but her time with the Reds and Blues and the events of the story tempers this. By the end, she's still pretty idealistic, but far more realistic and practical.

Rarity

Beware the Silly Ones: She's an over-the-top ham, but she's powerful enough to fight Tex on even footing.
Large Ham: She's very prone to melodrama.
Shell-Shocked Veteran: Her time in CT's custody leaves her with some PTSD.

Rainbow Dash

My God, What Have I Done?: She's guilt-ridden after O'Malley!Pinkie tricks her into helping her burn down the Carousel Boutique.

Fluttershy

Shrinking Violet: She's cripplingly shy and prefers to keep to herself.

Applejack

Odd Friendship: She and Sarge form a bond over their shared hatred of Grif.

Pinkie Pie

Birds of a Feather: Predictably, she and Caboose get along like a house on fire.
Church: Great, fucking great. I have two of them now.
Break the Cutie: O'Malley's possession of her really does a number on her. Caboose manages to get her out of her funk.
Cloudcuckoolander: It is Pinkie Pie, after all.
Demonic Possession: O'Malley possesses her soon after he gets to Equestria.
Weirder Than Usual: Her behavior after O'Malley possesses her takes a turn for the erratic and violent.

The Reds and Blues

Church

Private Leonard Church / Alpha

But Now I Must Go: He leaves Equestria at the end of the story to carry out the Director's last request, not wanting to be confiscated by the UNSC.
Character Development: Slowly goes from a selfish jackass who only cares about himself to a jackass who deeply cares about his friends and puts himself at risk for them multiple times.
Deadpan Snarker: Everything that comes out of Church's mouth is pure snark.
Heroic BSoD: After realizing he's the Alpha. It puts him in a sourer mood than usual and he oscillates between accepting it and fervently denying it until Tex proves it to him by shoving him into a computer. He gets over it eventually, deciding that, no matter his origin, he is still human in his own right.
Hypocritical Humor: He initially hates Twilight for being self-important and being better than him, whereas he actually is better than everyone else.
I Reject Your Reality: His reaction to learning he's the Alpha is an insane amount of denial.
It's All About Me: At first, he only cares about himself and Tex, and refuses to help Twilight because her being stranded in Repertum it's not his problem.
Jerk with a Heart of Gold: Church is an egotistical, snarky, cynical jerk, but he cares about his friend and gradually becomes more heroic.
Knight in Sour Armor: He develops into this as the story goes on. He's still a cynical jerk, but he'll still do the right thing.
Mirror Character: From Twilight. They're both beleaguered but Not So Above It All straight men who deal with an insane group that they call friends and both turn out to be forms of artificial intelligences. They wind up binding over it.
Only Sane Man: He and Twilight have to play this role among the Reds and Blues.
Sir Swears-a-Lot: Swears the most out of the entire cast.
Took a Level in Kindness: Gradually grows more heroic and friendly as the story goes on, particularly towards Twilight.
What Have I Become?: After discovering he's the Alpha, Church goes into a total meltdown and becomes even more bitter and antagonistic than usual.

Tucker

Private Lavernius Tucker

Brilliant, but Lazy: Tucker is a great soldier, but prefers to spend his time hitting on women and slacking off.
Everyone Has Standards: Even he wouldn't perform bestiality.
Jerk with a Heart of Gold: A snarky pervert who is also surprisingly respectful towards women when given the chance and has numerous heroic qualities.
Lovable Sex Maniac: He's a gross pervert, but he has some standards and can be surprisingly respectful to women.

Caboose

Private Michael J. Caboose

Birds of a Feather: Predictably, he and Pinkie get along like a house on fire.
Church: Great, fucking great. I have two of them now.
Child Hater: He has an inexplicable hatred of babies for whatever reason.
Cloudcuckoolander: He lives in his own little world and seems completely detached from reality.
The Ditz: It wouldn't be Caboose if he weren't a complete moron.

Tex

Agent Texas / "Tex" / Beta

"Could Have Avoided This!" Plot: Fluttershy lampshades that she probably could have just asked around to figure out who O'Malley is possessing instead of attacking everyone in sight.
Heel Realization: After Twilight calls her out on using Sunny and exploiting her trauma, Tex realizes she's starting to act like the Director.
Jerkass: The second she gets on Equestria, she starts beating the crap out of a ton of random ponies just to figure out where O'Malley is.

Sister

Private Kaikana "Sister" Grif

Cloudcuckoolander: She's very prone to saying bizarre and disgusting things at random, and she mistakes Twilight for a dog when she sees her for the first time. It's deconstructed, since it's eventually revealed that this is the result of her addictions taking their toll on her mental state.
Mirror Character: She used to be exactly like Fluttershy before spiraling into addiction.
Shrinking Violet: She used to be this, before her addictions drastically changed her personality.

Sarge

Sergeant Sarge

Kick the Dog: Mocking Grif about Sister's death. Even he realizes he went too far with that one.
Odd Friendship: He and Applejack bond over their shared hatred of Grif.

Simmons

Private Richard "Dick" Simmons

Birds of a Feather: He and Twilight quickly bond over their shared nerdiness.
Heroic Sacrifice: After being fatally wounded in a trap set by Project Freelancer, Simmons remains behind to hold off Freelancer soldiers and allow Church, Washington, and Twilight to escape.
Heterosexual Life-Partners: With Grif, though as per usual, the 'Hetersoexual' part is a bit ambiguous.
Nice Guy: The nicest of the Reds outside of Donut, and he's the first of the Reds and Blues to genuinely help Twilight out.
Sacrificial Lion: His death is what kicks off the Darkest Hour and signifies that things have really gotten serious.
Vitriolic Best Buds: With Grif. They bicker constantly, but they're absolutely inseparable.

Grif

Private Dexter Grif

Brilliant, but Lazy: Grif is a legitimately skilled leader and defeats Freelancer's troops with only one casualty, but he's also quite possibly the laziest being to ever exist.
Heterosexual Life-Partners: With Simmons, though as per usual, the 'Heterosexual' part is a bit ambiguous.
It's All My Fault: He blames himself for Sister's spiral into addiction, because he convinced her to date a guy who got her hooked on drugs.
Vitriolic Best Buds: He and Simmons bicker constantly, but are absolutely insufferable. Grif crosses the Despair Event Horizon after he dies.

Donut

Private Franklin Delano Donut

Going Native: Predictably, Donut assimilates very quickly into Equestrian culture.
The Knight Who Says Squee: He geeks out when Twilight arrives and bombards her with questions. He's even happier when he ends up on Euqestria, which is basically paradise for him.

Lopez

Karma Houdini: He never faces any consequences for killing Sister.
Sociopathic Hero: He shows no remorse over killing Sister, since he was programmed to win the Red-Blue War, and decided that was the most efficient way to do it.

Agent Washington

Agent Washington / David

Adaptation Personality Change: He's much more vocal about his disdain for Project Freelancer than he was in canon.
Anti-Hero: Washington is cold and ruthless, but is ultimately out to destroy Project Freelancer.
Character Development: He becomes less ruthless and loses his Well-Intentioned Extremist qualities as the story goes on and he realizes that the Mane Six and Reds and Blues consider him a friend, ultimately deciding to screw over his only chance of convicting the Director to bring back Twilight's memories.
Doomed Hurt Guy: He's severely injured during his battle with Maine, and the climax reveals he died of his wounds. The Spin-Off later reveals he survived and is currently in a new identity on Equestria.
My God, What Have I Done?: After he discovers Twilight had been fragmented after being tortured no-stop for days, he is overcome with regret for turning her over and profusely apologizes.
Well-Intentioned Extremist: He's willing to do anything to take down the Director, which results in him turning Twilight over to him to do so. He grows out of this afterwards.

Doc

Medical Officer Frank "Doc" DuFresne

Worst Aid: He manages to dislocate one of Twilight's legs while trying to pop a dislocated leg back into place and uses CPR and aloe vera to treat a bullet wound to the head (which actually works).

Equestrian Government

Princess Celestia

Princess Luna

It's All My Fault: She blames herself for Twilight being teleported to Repertum, since she had assigned Twilight to examine the ship behind Celestia's back. Twilight points out that, while she probably shouldn't have lied, none of what happened was really her fault.

Arcane Star

Butt-Monkey: He has a bad habit of getting violently interrogated by Freelancers.

Sunny Side

Tomb Reader

Ponyville

Spike

Spike the Dragon

Derpy

Derpy Hooves

UNSC

Project Freelancer

Leadership

The Director

Director Leonard Church

The Counselor

Counselor Aidan Price

Captain Osgoode

Captain Donovan

Walter Donovan

Cruel and Unusual Death: Maine breaks his back hard enough that there's a Sickening "Crunch!".

Agents

Agent South Dakota

Ignored Epiphany: She briefly shows regret for killing North, only to quickly try and justify it by claiming he was holding her back.

The Meta

Agent Maine / The Meta

Knight of Cerebus: Any time he appears, all humor disappears, and he ushers in the more serious plot along with Wyoming.

Agent Wyoming

Agent Wyoming / Reginald

It's All About Me: Everything he does is designed to benefit himself in some way. At one point, he outright admits that he decided a long time ago "that the only right thing is what's right for me!"
Killed Off for Real: After surviving his canon death, he gets definitively killed when the Mother of Invention's cannon fires on his ship and blows him apart.
Knight of Cerebus: Downplayed. He retains his humorous qualities, but his arrival causes Cerebus Syndrome to start.
Spared by the Adaptation: He survived his canon death here, having used his time-travel copies as a distraction so he could escape.

Artificial Intelligences

Delta

The Spock: Emotionless and prone to citing logic.

O'Malley

O'Malley / Omega

Affably Evil: He can be remarkably pleasant for a psychotic, rage-filled AI.
Ax-Crazy: Gleefully psychotic, makes numerous brutal and absurd threats, and tries to burn several Ponyville residents alive For the Evulz.
Heel–Face Door-Slam: After Pinkie manages to get through to him, he gets assimilated by the Meta.

Sigma

Faux Affably Evil: He's pleasant and chatty while talking O'Malley into allowing himself to be assimilated by the Meta.
Small Role, Big Impact: He only appears in one scene, but he drives the Meta's actions throughout the story, even after his death.

Gamma

Asshole Victim: After he spends his screentime trying to kill innocent ponies For the Evulz and because of Fantastic Racism, it's hard to feel bad when he gets assimilated by the Meta.
Ax-Crazy: He tries to murder Arcane Star and his archaeologists For the Evulz.
Fantastic Racism: He's implied to have this for Equestrians, which helps with his eagerness to murder them.
For the Evulz: His attempts to murder the archaeologists and teleportation of Twilight seem as motivated by amusement as it is his desire to escape the Meta.
Small Role, Big Impact: He only appears at the beginning and is assimilated by the Meta before he can do much, but he is the one who teleports Twilight to Repertum, setting off the events of the story.

Simulation Troopers

Captain Mogar

Captain Mike Mogar

Not Quite Dead: Survives being shot in the head by Caboose thanks to Doc giving him CPR and aloe vera.

Captain Reynard

Captain Reynard Naez Jr.

The Mad King Hayworth

Captain James "The Mad King" Hayworth

Associates

Sunset Shimmer

Gilda

Gilda Graywing

Silversteel

Cruel and Unusual Death: Maine beats him and then crushes his head.

Commander Graywing

Characters / I Against I, Me Against You

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