After the airship armada. Things in Equestria were not at all good. After Bowser settled in, he totally rigged the place completely, he made the all the ponies in Equestria his slaves, and he put taskmasters over the ponies to make sure that they will rebuild everything destroyed the airship attack, and things were not good at all, the ponies groined under their heavy and brutal burdens. They wanted to be free again, have the royal sisters and sister-in-law back, for they couldn't believe they were gone for what could be for good.
Bowser made the water turn into lava, and also had things a lot like his own way. He hated the old ways of Equestria, and turned the ounce happy and free nation into a weak, sad, and enslaved nation, and soon many feared their new ruler, the only free things were that zebra in the everfree forest, Twilight's assistant, Spike and her pets, and Fluttershy's pets, who Bowser let them have the enslaved ponies riches. But all of them refused.
Spike missed Twilight, he was dumbfounded when he heard that Twilight was not only captured, but severely injured, and couldn't believe that whoever that monster was thought he could just let his son lead his armies against Equestria and conquer it, and then have the country ruled his own way, did he do this with his own subjects? No!
Spike paced in the library angrily. He knew if he was going to try to overthrow the monster, he needed a companion that knows how to defeat him.
Meanwhile, Yoshi, Mario's companion to help him get past some really tough obsticles, searches for Bowser, he knows he is causing trouble somewhere, he can sence it in his bones.
When he entered the country called Equestria, his eyes widened in alarm, someone took over the place, enslaving the inhabitants, Yoshi then feels a urge to move into the country, his mind raced furiously. "Bowser, I'll get you! I'll get you for this!"
Yoshi then found a town where he found a baby dragon talking to himself.
"Okay, so if I somehow sneak on one of the airships, then I'll be able to kill that monster and his son who leads the army."
"Not a good idea."
"Huh? AHHHHH! DON'T HURT ME...oh, I thought you were that monster." Said Spike, still trying to recover from the sudden apperence of Yoshi.
"You mean Bowser? Well, me and my buddy Mario fight that guy, A LOT!!!! Ever sence we were kids we were fighting that ugly beast."
"Wait, you...KNOW HIM?!!!!"
"Yep, I know all of his weaknesses and strengths, and I can see he got real power hungry when he conquered you guys."
Spike began to frown. "Yeah, let his son lead an army of thousands, capturing our princesses and my friend, who is one of the princesses as well, they severely injured all of them, so badly that they were blacked out."
"What?!!! Bowser Jr. did that to them?! Where are they?!"
"Took them away somewhere. But first I want to pretty much overthrow the monster."
Yoshi thinks the baby dragon will get killed if he attempts such a thing, but he knows he could help. "You can't fight him on your own, especially because you don't know how to avoid his strong attacks and knowing how to defeat him. But I do, I'm helping."
Spike knew the green dinosaur was right, no matter what, he needed his help, besides, if Twilight found out if he was dead, she'd try to overthrow the monster and get killed.
"Alright, but we also have to find the princesses as well, and free them, that way, Equestria would be happy and free with the princesses ounce again."
"But one last thing, you see, in every adventure I had with Mario, we had to destroy the fortresses that guarded our path from moving towards Bowser. I'm sure we'll have to go to each town and city, starting with the one on the border between Bowser's castle and country, and this one, that way we can be sure that if Bowser hid keys in the fortresses to unlock a barrier between us and him, we can unlock it."
"Sounds confusing, but okay!"
"Hop on my back little dragon!"
So the duo had started a journey to free Equestria and the ponies who were enslaved to the evil monster and his son, their first destination was the desert town, Appleloosa, and the two unlikely heroes start towards the southwest.