The fact that every nation on Earth puts their differences aside to fight for the survival of humanity is awesome in itself. Most especially amazing is how every country in the Middle East bands together against TCB!Equestria.
Princess Celestia declaring that Equestria will go to war against its evil mirror to help humanity.
Queen Elizabeth: You think you can come into MY palace, MY country, and destroy the will of MY people! I may be old and decrepit, but I. WILL. NOT. STAND FOR THIS INSULT!
PER Agent: Potion the bitch!
Queen Elizabeth: I think not. Say goodbye to the world, and may God Almighty show you the mercy I withhold!
It is said that upon getting potioned, and while already half-ponified, Prime Minister Rokubungi of Japan committed seppuku with a severed unicorn horn taken from one of his attackers.
The fact that humanity is willing to set off the Yellowstone megavolcano, effectively killing us all, rather than surrender to the Queen and live as brainwashed slaves to a xenocidal tyrant.
Chapters 6 and 7, both parts of "The Answer", follow TCB!Trixie in action as the Blue Spy. Cue some of the most well-written and engaging scenes in the story.
In his brief appearance, TCB!Fancy Pants proves he is still one of the finest members of Canterlot society by serving as The Mole. Even better, he does so by posing as a flower seller assisted by Roseluck, Daisy and Lily, whom it would seem are cowardsno more.
Trixie's interrogation of Green Fields, a former member of the Royal Guard, is quite harsh and unpleasant, but it all turns out for the good when Cadance successfully uses The Power of Love to free him from his brainwashing.
Using a mix of cleverness, stealth and brute force, the Blue Spy infiltrates the Castle of the Two Sisters, which has been repurposed into a top-security prison. Admittedly, The Guards Must Be Crazy is at work a good deal of the time... until the Spy encounters Focus Ray, who in spite of being a Newfoal proves to be almost more than she can handle. Almost.
Trixie's whole fight against Focus Ray counts, really. They engage in a verbal confrontation as well as a physical battle when Ray tries to persuade her of the Solar Empire's righteousness. She rebuffs his argument by willingly using herself as an example of why ponies aren't perfect. Yet despite struggling with her fractured mental state and the effects of a poisoned knife throughout the battle, Trixie resists the urge to kill him right away, hoping that he can still be saved. Sadly, her Spy persona eventually takes over and puts him down.
The Big Damn Heroes towards the end, when who else should arrive but for Doctor Whooves and his family in the TARDIS? And as with Fancy Pants, Derpy makes the most of her limited screentime by gently coaxing a broken and mutilated Spike out of his Heroic BSoD, then later single-hoofedly holding the TARDIS's doors shut to the Guards. Plus, when the Doctor gets injured by Focus Ray, Trixie draws away the Newfoal's attention by assuming the shape of none other than LyraHeartstrings, friend and defender of mankind. In a fic which often aims for the big and dramatic, it's these small moments that really stand out.
Queen Celestia is too late to stop the heroes from rescuing Spike, but they did leave her a grenade and an insulting note.
Princess Celestia delivering a long overdue and very well-deserved verbal beatdown on Prince Blueblood in Chapter 11.
Thanks to the efforts of human and pony doctors, Scootaloo will finally be able to fly.
TCB!Cadance becoming a full-fledged alicorn, along with Cheerilee receiving the gift as well (and every other pony and human present, for that matter).
The Scribe is a virtually immortal construct of nigh infinite wisdom and knowledge but also possesses amazing compassion and kindness. Her gifts to the PHL members are nothing short of amazing (even if none of it actually happened).
TCB!Scootaloo deciding to join the fight despite losing her wings and promising to take down her former hero Rainbow Dash.
And then the TCB!Cutie Mark Crusaders are reunited, and they all finally get their cutie marks.
TCB!Lyra's posthumous speech. Bonus points for referencing Charlie Chaplin's speech from The Great Dictator, aka "The Greatest Speech Ever Made."
Chapter 13 has Prime!Luna appears before a group of fighter jets led by King William and declaring their intentions to aid Earth.
Also because of this cameo, we can assume that other badasses such as Niko Bellic and Luis Lopez are also fighting against the TCB!ponies.
Prime!Discord disposing of their universe's Bag of Tirek by throwing it into space.
Even better: when tempted with "anything he asks for", he pulls an Inigo Montoya by asking the Bag to bring back his mother from the dead.
Kraber gets more than a few in "For Whom The Bell Tolls". He doesn't kill the Elements. But he does come damn close, managing to survive at close range in a knife fight with TCB!Pinkie Pie and kick her in the face. On top of it, he takes a three-story fall, a blast from Pinkie Pie's party shotgun, and a display case to the gut, and shrugs it off with minor injuries he doesn't notice for hours.
In the chapter titled 'Strike', Queen Celestia gets a very good taste of her own medicine.
The chapter 'Trust' follows those above-mentioned moments with these...
Luna, despite transforming into her Superpowered Evil Side, is in full control of herself, as she delivers one heck of a beatdown on the Celestia clone.
Kraber destroys the Celestia clone's spine with a well-placed shot from a DSR.50!
Stephan not only faces down Celestia's clone by himself, but he gets up despite the strain the fight puts on his body, and then slices her up in half with his claymore.
Arguably, Queen Celestia gets one herself for sending in a double, which is smart enough to nearly prevent the humans from trusting Luna. On a meta level, the fic manages to have its cake and eat it too by providing readers with plenty of catharsis before knowingly subverting Villain Decay.
While the world's military leaders debate whether they can trust Prime!Luna and Discord, US President Jack Davis unloads a big speech against them and spells out very clearly that humanity just has no options left at this point. The leaders decide to give the two a chance.
Princess Celestia stepping up with resolve, admitting that the last few days have been very tryingon her body and mind, but is now more than willing to step up and be the leader Equestria needs and deserves. And there's her Rousing Speech to the Crystal Ponies, giving them the drive to power the Crystal Heart and get rid of Sombra, permanently.
'Training Days: First Days )Part 1)': Luna keeping a cool head, even giggling, at a dissenting Royal Guard's assertion that humanity will betray the Canon!Equestrians and his baseless accusations of her still being Nightmare Moon. Shining Armor then unflinchingly orders the soldier to leave and boots him out.
'Training Days: First Days (Part 2)' has every army on Equus pledging to fight to its fullest for humanity. Sint Erklass' Rousing Speech, comparing the Solar Empire's ruthlessness to The Terminator stands out especially.
Near the ending of 'Training Days: The Second Month', Catseye is visited in a dream by Queen Celestia... which is then hijacked by the spirit of TCB!Lyra, trying to plead with Catseye to see reason. Queen Celestia then summons a construct of Dr. Reitman, and the two have a rather personal debate on whether humanity deserves to be saved or not, in a Good Angel, Bad Angel exchange of words. To sum it up, even though Catseye refuses to listen to Lyra and the Reitman construct simply just sticks her head in the sand and responding to Lyra's Armor Piercing Questions with personal insults, Lyra bows out with dignity right after giving them both massive The Reason You Suck Speeches.
'Invasion Plans' reveals the existence of a homegrown Resistance Movement on TCB!Equestria who are just as dedicated to stopping the Empire as everyone else; it's just that they and the PHL don't always get along due to some conflicting interests. But then Cheerilee finds out what they have planned to help the PHL's invasion in the final battle... Harshwhinny and the resistance (also known as the New Lunar Republic) have plans that will cripple TCB!Equestria: cutting telegraph lines, stopping railroads, shutting down the weather factory, taking out high ranking officials, and slaughtering newfoals by the the thousandfold. As Harshwhinny puts it, they're rolling out the welcome mat for the PHL, and more than likely guaranteeing their success in doing so.
Celestia and Luna's World of Cardboard Speeches at the end of "Of Broken Pasts". Upon being told by Fancy Pants and Lady Flare that Stephan has been captured by Catseye and her followers, the alicorn sisters declare that ponykind is not above reproach, nor will such acts of arrogance be tolerated ever again, not to mention that betraying humanity's trust in and of itself is a monumental mistake.
Except it's then subverted by the events of "Only Human", in which Berry Punch dies because of the Blue Spy's brainwashing-induced rampage through Ponyville. A later scene in the "Pale Moonlight" arc has Luna regret going into the speech too hastily, while Celestia hints that she was putting on a facade. (VoxAdam states he was not a fan of the speech scene.)
When a projection of the Blue Spy corners Prime!Chrysalis in the dreamscape, proceeds to demean her, calls her a "fake" for being less accommodating than TCB!Chrysalis, and employs some Changeling-based magic to try and overshadow her, how does Chrysalis respond? By catching her opponent completely off-guard and eating the Spy in one gulp.
Queen Chrysalis: So, tell me, little pony. Who's the poser now?
A retroactive one for the characters of the Asia Side Story. By the time of "Trust" in the main story, their callsign is the Dragons of the East. No doubt they earned that nickname by doing something right.
TCB!Fancypants gets found out as a spy by Fleur. She initially refuses to go along with it, but when a bunch of newfoals try to kill them, Fancy pulls out a multitude of swords, slicing newfoals up and down before getting his newly-revealed-to-be-pregnant wife out of the house. Queen Celestia then shows up there to dispose of Fancy Pants personally, and Fancy proves to be Defiant to the End, calling her out on her Suicidal Overconfidence before using an enchanted Griffon katana to blow up the house.
In the PHL chapter, we finally find out what happened to the Thunderchild warship during Lyra's Last Stand. And it was brilliantly badass.
Last Train From Oblivion
Chapter 3 includes this gem:
Lightning Dust's hallucinogenic vision of Lyra, now a regal alicorn, fighting the Solar Tyrant for mankind's soul, while the Scribe looks on from above. It's a simple, obvious image, yes, but it says more than a thousand words could about just how much is at stake, and what Lyra Heartstrings meant to humanity.
The Light Despondent
Remember how dangerous the Pretty Privates were built up to be, specifically in Last Train? Kraber gets in a fight with a prototype version of a Pretty Private with dual shotguns, ridiculous durability and shield spells, and the ability to resurrect the dead. It breaks his leg and arm, making him only able to limp away... and he manages to get to a sympathetic unicorn, heals himself up, and kills it.
As noted in the author's notes, Kraber's reaction to meeting the personification of his own guilt is to suplex it and throw it at a wall.
Nebula telling off the unnamed interviewer in Chapter 10, telling him that they shouldn't resort to horrible and disturbing projects such as reverse-engineering Reaper's necromancy.
Nebula: They've only gotten far because of how they can deequinize, turning ponies and humans to tools, seeing flesh as building blocks. I was around for the first newfoals! I saw how far they can go. I'll be damned-
Nebula: As I was saying, I'll be damned if we win because we can be bigger bastards than the other guy. Now why don't you ask me a question that's fucking well related to what you came here to ask?
Best of all, this gets him to listen!
Shades of the Unsung
Although Rockwell fails to free her, TCB!Rarity swears to continue resisting and fighting back against her homunculus and free herself someway, somehow, someday.
The sheer fact that Rockwell managed to badmouth Queen Celestia in her mindscape, while also having the balls to call her out, and survive is just plain badass in and of itself.
The ragtag group of the Mamayev Kurgan successfully managed to stop a raid from the SAS themselves. While most of their action is done offscreen, a highlight of their victory is the fact that they managed to shoot down the SAS helicopter first.