Bittersweet Ending: Discord is defeated in the end...by Church trapping him inside his mind and letting himself be turned to stone. Sure, Equestria was saved, but now Church is gone.
Brilliant, but Lazy: Grif, in this fic, isn't just competent when not lazing around but also exceptionally kind, even going into the Everfree Forest to look for Fluttershy's lost bunny despite knowing how dangerous it is.
Butt Monkey: Grif, perhaps even more so here than in the series, even when he's trying to be nice or didn't do anything at all. Examples include getting attacked by Timberwolves when he tried to save Angel, and having Tex beat him up for literally no reason other than that she was bored.
Call Back: In an early chapter, Caboose draws a rather crude crayon sketch of himself and Church as ponies. Church finds the picture to be rather awful. Later, after Caboose dies, he's found mourning over his death and staring at the same picture.
"Memory is the key."
The joke from Red VS Blue where Grif brings up how Sister once fell through the ice is brought up again... and deconstructed somewhat, as we get to see a flashback of Grif witnessing the event, revealing it to apparently be rather traumatic for him, and serving as a Chekhov's Gun that pushes him to save Tex from a similar fate.
Also, remember back in Red VS Blue when Grif brought up how Sister once fell through thin ice and came up unharmed and pregnant? That gets brought up again and motivates Grif to save Tex from drowning.
Cursed with Awesome: After suffering a Timberwolf bite, Grif's strength, speed, and endurance increases because of the tree DNA now in his system.
Dark Is Not Evil: The Necronomicon, an evil-looking talking book that was locked away because it has the power to raise the dead. Turns out he's actually a fairly decent guy, if a bit of a smartass. It's just the ponies that used him before that were evil and caused him to be locked away.
Think Andy (the Bomb), but muted a little (and not exploding).
Deadpan Snarker: Church, Delta, Tex, and Applejack seem to be the primary examples.
Although all of the Blood Gulch Crew and much of the rest of the cast all qualify at one point or another.
Death Glare: Sarge when told he said something that Grif would have.
The Drag-Along: Church, and to a lesser extent Twilight, during Pinkie, Caboose, and Derpy's quest for ingredients to create "muffcakes". He makes himself very vocal about disliking this, and eventually leaves after he gets eaten by a Hydra and blows it up from the inside using his magic.
Good Is Not Nice: The red and blue teams may be on the side of good, but the majority of them aren't exactly kind. Only Caboose and Simmons are actually nice most of the time. However, most of the Rooster Teeth-based cast do mellow out over the course of the story.
Heroic BSOD: Church gets one after Caboose's death. As do the rest of the RVB group. But most of all, Pinkie Pie, whose hair straightens out.
Twilight is in love with Church, but he's still stuck on Tex. He does respect her as someone he trusts and as one of his first real friends, though. There's also some teasing between Fluttershy and Grif.
Took a Level in Kindness: The usually cynical Blood Gulch Crew become more pleasant in this world. Especially prevalent with Tex, except for when dealing with Grif. Towards the end of the story, they do start to get along better... somewhat.
The kindness is relative, though, by which we mean "They're still jerks to one another, but not actively trying to kill each other."
Most of the time, at least.
Wham Line: Quoth Applejack: "She ain't never said anythin' 'bout us bein' able to trust th' Epsilon fragment."
And then later: Tex, reading a letter: "It's from a guy named Discord."
And then even later: Discord, referring to Tucker, Church, Sarge, Simmons, Grif, and Tex: "Give it up for the Elements of Chaos!"
What the Hell, Hero?: Church really chews out Celestia after Caboose is murdered by Carolina and nearly gets killed for it. He's hated Celestia since then.
Celestia TRIES to call him out over Twilight's unrequited love for Church and how it's hurting her, but it's not successful.
Would Hit a Girl: Grif doesn't even hesitate to tackle Tex to the ground. Justified, as the reason he did that was because she attacked Fluttershy.