@Algebroot Neogears  
Well, the summary in the back cover of the DVD or blu-ray says that the Storm King did threaten Ponyville because it’s true that he ruled Ponyville and the rest of Equestria. I mean look at Ponyville after the song “Open Up Your Eyes.” You can see smoke hissing above Ponyville while some of the airships of the Storm King’s armada are heading towards Canterlot. Ponyville is likely on fire. But, I bet some of the ponies in Ponyville, who are about to go to Canterlot of the Friendship Festival were enslaved, or captured, or imprisoned, or punished by the Storm King and his Storm Forces. And I bet even Mayor Mare was locked in a cage in Ponyville by the Storm King and his army. Just like what Trixie did while ruling Ponyville in “Magic Duel.” I bet like Trixie in “Magic Duel”, the Storm King did forced the remain citizens of Ponyville to become his slaves like the ones in Canterlot. And I bet they have Storm King banners like in Canterlot and maybe there were some statues of the Storm King. The summary of the back cover should have said either “Equestria” or “Canterlot” instead of “Ponyville.” This is my opinion to what in Ponyville during the Storm King’s invasion/ruling of Equestria while the Mane Six were gone during the movie.

@northern haste  
There’s also “the Mane Six goes on a journey”…
 
There seems to be a revised description in the 25th anniversary collection. Some parts are corrected, but the “Ponyville” error remains:  

 
pretty sure it was all of Equestria that was being threatened  

 
pretty sure they left Equestria  
edit:oh God I just check that actually what the official Blu-ray says