I have 2 ideas.
1.) someone write a petition for Hasbro to change their mind about airing that rejected Big Macintosh-focused episode.
2.) have the Season 3 finale involve a 4-part epic where Equestria gets invaded by an army of Roman-style Pony Legionnaires lead by a ponified Julius Caesar expy who manages to annex Equestria forcefully, kicks the Princesses and royal guard out of Canterlot, and manages to destroy the Elements of Harmony, prompting the Mane Six to go on a 2-way journey to:
A) Figure out how to repair the Elements of Harmony
B) helping a group of rebels lead by Princess Celestia and Shining Armor, who end up having to forge a rebellion against the Pony Legionnaires.
Also, in stark contrast to Discord, who likes to bring Equestria into chaos, the aformentioned Ponified Julius Caesar (feel free to come up with any name you see fit, though I'd personally call him Legaticus Egoticus) would be a villian who favors order over harmony, and as such, could be a Knight Templar uptight tyrant who'd put Equestria under martial law and functionally bullies its citizens.
If you think about, it would be a season finale that involves Twilight and her friends going against the Roman Empire, can anyone here think of a more badass epic story?