StarTrixBurst Squad Saga (Episodes 1-12) Various popular non-Mane Six ponies, including the STB Squad protagonists Starlight, Trixie, and Sunburst, have moved to a futuristic city of adventure known as Ponyopolis. Twilight Sparkle, under the influence of the hidden main antagonist Master Element, is creating monsters and robots and casting spells to hinder daily life in Ponyopolis. After the STB Squad destroys the first monster, Trixie accepts the Ponyopolis Defense Force's offer to join it for further excitement and brings Starlight and Sunburst with her.
Sunset and Moondancer Saga (Episodes 13-32) Moondancer and Sunset join the STB Squad and point out that Twilight has a really bad habit of abandoning and forgetting about old friends. After reading about the Elements of Harmony, Twilight moved to Ponyville without telling anyone. As a result, she deliberately skipped Moondancer's party and broke her heart. Also, after Sunset stole the Element of Magic and took it to the human world, Twilight abandoned her and forced her to live there without magic.
With the help of Moondancer and Sunset, the STB Squad uncovers a massive conspiracy that involved Master Element creating the Elements of Harmony from his own essence to manipulate Twilight into being his second-in-command, and using special effects (with an entire special effects team) to create fake villains whose "attacks" were staged to make everyone lose brain cells, sit back, and let the Elements "save the day" (in a similar way to the movie version of Spider-Man's Mysterio).
For the final battle of this saga, Sunburst builds a portal generator that, unlike the mirror portal of Equestria Girls, lets its users go to the human world without being transformed. That way, Moondancer, Sunset, and the STB Squad can fight Twilight outside of Ponyopolis to avoid collateral damage. Then when Twilight is defeated as Giant Midnight Sparkle, the resulting explosion destroys the human world completely (the main unicorns survive said explosion by all shielding each other at the same time).
ReManeing Five Saga (Episodes 33-44) Twilight has been defeated and snaps out of the corruption resulting from using the Elements. She must now adjust to life in Ponyopolis with the help of both the main unicorns and the supporting pegasi Lightning Dust, Daring Do, Derpy Hooves, Sky Stinger, and Vapor Trail.
But the battle is not over yet. Master Element has now taken control of Twilight's Ponyville friends and Canterlot family as well as Celestia and Luna to attack Ponyopolis. Twilight joins the ten pony heroes to help them cure her own friends and family of Element's corruption.
But Ponyopolis's population is convinced that Twilight's magic of friendship is a hindrance. Is she still relevant in the post-FiM era?
Master Element Saga (Episodes 45-52) All the ponies involved head for Element's headquarters for the final battle against him (not just a one-hit blast of friendship, for those don't work on him). Father from Fullmetal Alchemist: Brotherhood is this saga's icon because Element's final battle is similar to Father's: Like Father, Element starts out in his strongest form with all the heroes fighting him at once and must be gradually stripped down to his bare essentials so Trixie can Falcon Punch him into oblivion.