Awesome / The Elements of Harmony and the Savior of Worlds
Rainbow Dash and Twilight Sparkle, albeit by accident, created a new connection between Earth and the world where Equestria lies.
Megan. Founded. Equestria. She brought the various scattered groups of ponies together, helped weave alliances between them. She brought a ton of books over to provide them with information that was invaluable in building their civilization. She, Molly, and Danny raised Luna and Celestia for the first part of their lives. And that is how Equestria was made.
Maybe at the end of the story, Pinkie Pie can tell us how she got her cutie mark. It's a gem!
Fluttershy tries to use The Stare on Spykoran the Old after his dramatic entrance scares a bunch of ponies and Megan's kids, and he shrugs it off. Giving him further Badass points, he then proceeds to effortlessly trounce the green dragon causing trouble in Everfree forest.
Better? Later it turns out Tirac himself is incapable of just shrugging off the Stare. That's how badflank Spykoran is!
From the sequel, Omnicorn Megan: 1/5 earth pony, pegasus, unicorn, flutter and sea pony, half-crazed, half-angry, and 100% focused on taking down TCB!Celestia, as soon as she fights off that pesky brainwashing.
Ironically, if there's anyone more deserving of being an alicorn, it's Megan herself.
As of June 3, 2013, the most current chapter has Optimus Prime on his way to help save humanity from TCB!Celestia. He even put the Autobots and all Autobot forces on Earth in control of the EDC until he gets there.
Danielle and Michelle putting Diamond Tiara and Silver Spoon in their places for bullying the CMC, even shooting down their "I'll tell my daddy" backup plan by pointing out that they're the adopted sisters of Celestia and Luna.
The Reveal of the true villain of the fic: Tirac is back!
Celestia versus the Ursa Major.
Celestia gives Mike a suit of armor, and later magically upgrades his rifle to shoot lasers.
Trixie showing up just in time to save the CMC from one of Tirac's Ursas, managing to successfully fight it off long enough for them to escape.
In the side story "Day of the Broken Fang", Cobra Commander telling off Serpentor when the new leader of COBRA confirms that he ordered an attack on the Decepticons, and then being Genre Savvy enough to get the hell out of there thus being one of COBRA's few survivors.
During the Final Battle, Tirac summons the Rainbow of Darkness to hold off the Elements of Harmony, and does so successfully... until Megan shoots his arms off, disrupting the Rainbow and allowing them to destroy him for good. And then the Elements' wave spreads out and destroys all of Tirac's Shadowbolts.
The individual efforts by each of the Mane Six during this fight also deserve mention, even if they didn't accomplish much.
Special note goes to Fluttershy nailing Tirac with the Stare and it actually effecting him.
Luna killing the last Ursa by shooting it in the head.