The ponies and the Nord woke up...
"Hey you, you're finally awake" The Ponies heard from another carriage, a man was talking to their new friend about crossing the border or something, their hooves were tied, when they arrived in Helgen, they saw someone get their head chopped off, their friend was next, but then Alduin returned! They followed the Nord and Ralof into the caves of Helgen, they got untied, same as the Nord, the ponies and Ralof with the Nord went their separate ways. They went to Riverwood to sleep at an Inn, a few days later, they hear about another Dragon, at Western Watchtower, they go to there and help out Whiterun kill it, then the Nord started Shouting "FUS RO DAH!" over and over again, the guards were calling him Dragonborn, the ponies and Nord were confused, the guard explained the Dragonborn to them, the ponies started calling him Dragonborn for now on
"So what now, Dragonborn darling?" Asked Rarity
"We're going to White-" Dragonborn was about to say that they're going to Whiterun, but then hears
"DOVAKIN!!" He is confused and told to go to High Hrothgar, they do so. The Graybeard explains the whole Dragonborn thing, and asks why he has ponies following him around
"These are my friends...I guess?" He replied, the whole training thing happens, if you want more detail just play Skyrim. He is told to get the Horn of Jurgen Windcaller, he and the Mane 6 go through the caves, to find a note, telling him to go to the Sleeping Giant Inn.
Meanwhile where the Background 6 are... they're in Riften, apparently, Lyra thought it was a good idea to join the Thieves Guild, now she got put jail.
"Mind explaining yourself, Lyra?" Asked Doctor Whooves
"I was just bored!" Said Lyra, they break Lyra out, and see The Dragonborn and Mane 6
"Ah, Twilight, everyone you're here!" Said Doctor Whooves
"What are you doing here?" Asked Rainbow.
"Looking for you. What are you doing?" Asked Derpy
"Trying to find a blades member before the Thalmor do." Replied Pinkie
"Wanna join, Darlings?" Asked Rarity.
"Sure." Replied Bon Bon, they go through the Ratway and find the Blades member, Esbern. They continue to do more of the Main Quest of Skyrim, they meet the good dragon, they fight Alduin, they put a peace treaty between the Imperials and Stormcloaks, this is much different and faster as Fluttershy was cute about it, so they went "Awwww" And stopped, Ulfric Stormcloak and Titus Mede II hugged each other, more the same except extra ponies, until they reached Sovngarde...
The Dragonborn meets the 3 ancient heroes, at the same time, the ponies meet their ancient ancestors, Twilight, Surprise, Firefly, The original Applejack, Posey and Sparkler, and they get ready to kill Alduin once and for all. It takes alot of magic, alot of arrows, alot of kicking, even a sonic rainboom or 2, but Dragonborn finally killed him, destroyed Alduin, and ended his threat to Tamriel and Equestria, they get back, They're all rewarded greatly, the ponies return to Equestria, but the ponies keep in contact with The Dragonborn, thanks to a call spell that Twilight created.
This is where the journey ends for now...The end