Here is how the ending and Zod and Dark Eagle release Dark Ultron goes in Code Red's Adventures of My Little Pony Equestria Girls.
(We then see the ponies waiting by the mirror until Twilight and Spike come through)
Everyone: Twilight!
Twilight Sparkle: Not just me.
Sunset Shimmer:(appears from behind Twilight with a guilt ridden face)
Princess Luna: Come everyone, we must let these two catch up.
(Out in the hall)
Applejack: Hoowee! Who knew that the other world was really Earth the whole time.
Rarity: It's very surprising. But where's Flash Fire?
Twilight Sparkle: He's in the safest hands I can trust.
Sunset Shimmer: He went rogue. But Code Red will protect him.
(Sunset zips back to the portal)
Twilight Sparkle: Where are you going, Sunset?
Sunset Shimmer: Back to CHS, Twilight. I got some unfinished good things to do, Princess.[disappears through the portal]
[Twilight waves "Goodbye" to Sunset]
[the credits roll with "Sweet Dreams" playing]
(we see Dark Ultron lying down in the Phantom Zone)
(a portal opens and he goes through)
(On the other side is Zod and Dark Eagle)
Dark Eagle: Lord Thanos summons you.
Dark Ultron: Who's Thanos?
General Zod: In time you will see.
(movie ends)