Twilight keeping the Gate open, by herself, long enough for the rest of her party to get through it, is definitely her greatest achievement in the story thus far. The reason it's so awesome? First, keep in mind that the Gate weighs several hundred tons. Next, realize that it took the combined effort of Twilight, Rarity, and Tick Tock to even open it in the first place. This whole event is then followed by Rainbow Dash scooping Twilight up and flying through the Gate as it's closing and making it to the other side just before it does.
Havocwing, Grayscale Force, and Red Velvet arriving in the nick of time to save Twilight and co. from a swarm of Gargantuans solidifies the three of them as Badasses in the eyes of both readers and the Mane Six. Remember that young Gargantuans are larger than a manticore, and are armed with scythe-like claws and a deadly, poisonous sting; then remember that the adult in the group is bigger than an Ursa Minor, enough to crush a house with one of its many legs. Simply not being afraid of them is awesome by itself
Tick Tock opening up a barrage of taunts and insults against Starlight Shadow in a bid to get her to release enough magic to activate her Time Keeper's time-stopping spell goes to show that Tick Tock is, when confident and equipped, incredibly Badass. Starlight Shadow is powerful enough that the magic blast she fires rips through a mountain of solid gold, tears across the northern skyline, and launches off into space; all of this is seen from Pandemonium City. Tick Tock goads Starlight into firing this at her, and everypony present thinks she is crazy and stupid. But as she says later, she's crazy, sure, but not stupid.
Pinkie Pie's Badass Boast to Red Velvet in their second fight, declaring that (a) She's not afraid of Velvet, and (b) Since her powers rely on her being happy, the thing that would make her happiest is kicking Velvet's butt. Their fight that follows is a rapid-fire series of awesomeness between the two of them, with the highlight being Pinkie's Hyper Combo EX Burst Falcon Punch.
Grayscale Force demonstrates just how much control she really has over Gravity, using it to create a vacuum in an enclosed space with Applejack, forcing Applejack to give her back the advantage of open air, or they both die. Given her character, she probably would've gone through with it too.
AJ gets an awesome moment during both encounters with Grayscale. During the first fight she's the only pony capable of forcing her way through Grayscale's gravity power, and during the second she manages to make Grayscale admit that she's not a boring opponent. Given the list of things Grayscale finds interesting, (read:not a lot) that means a great deal
Rainbow Dash redeeming herself and re-aquiring her Element of Loyalty, then using her increased powers to turn into a lightning bolt, is definitely her highest moment in the entire fic.
Chapter 25 is pretty much one big CMOA for Silvertongue. First, with the help of the Mean 6, he manages to rip through from one dimension into the next and pull a goddess through, forcing her into a mortal form. Then he reveals that he'd managed to decieve and plot behind the back of Nihila (The GODDESS of deception who has direct access to his thoughts), for over 800 years, laying the groundwork for his betrayal before he'd even started working for her. The chapter culminates with him KILLING the allmighty Goddess and absorbing her power, turning into a god himself... wow.
Twilight Sparkle performs major surgery in Chapter 28. Without a license. She did have a licensed and incredibly skilled surgeon with her to help guide her actions, and didn't have to actually perform any incisions herself, but it's still astounding that she was able to go through it all, especially under all the pressure she had pressed upon her.