Dr. Whooves sent the TARDIS straight for the past in Canterlot. This was the location of Shining Armor and Cadence's wedding. The leader of the changelings, Queen Chrysalis, however, had other plans for them and had trapped Cadence underground. Chrysalis then took Cadence's form and was using Shining Armor's love for Cadence to overpower Princess Celestia. The TARDIS arrived right outside the castle and they could hear Cadence singing something about this day being perfect. They did, however, know that at this point, the real Cadence was still underground so this had to be Queen Chrysalis.
"Alright, everypony out. We have work to do. We can't let anypony see us and if somepony does, we must act as if we are from this time and know nothing of future events that are to transpire with the wedding. Understand?" ordered Dr. Whooves. Colgate nodded. "What does transpire mean?" Derpy asked. "Just don't say anything." Dr. Whooves replied. The trio got out of the TARDIS and headed to a window in the castle. They could see the Chrysalis Cadence laughing maniacally. She turned around and the three immediately ducked down so she wouldn't see them. They went around and entered the castle through the main entrance.
Dr. Whooves told the guards that they were there for the wedding and they let them in. Once inside, all that was left was for battle to begin. "We came here a little too early so we must wait." Dr. Whooves told them. Everypony gathered in the wedding room. Chrysalis Cadence and Shining Armor were about to get married when the real Cadence suddenly burst in with a purple pony who Dr. Whooves knew to be none other than Twilight Sparkle. "That's Twilight Sparkle. She's a very important part of this plan, I'll tell you more later." Dr. Whooves whispered to Derpy.
Soon, the Chrysalis Cadence was changing into her true form. Black with holes in her. She began to have a fight with the Princess Celestia and Chrysalis won. Derpy cringed at seeing this for a second time but nopony seemed to notice. That's when havoc begun. An army of changelings flew in and started attacking the ponies although there were six who seemed to be fighting back. Dr. Whooves looked to Derpy. "Those are the ponies that represent the six elements of harmony: Loyalty, Honesty, Kindness, Laughter, Generosity, and Magic. They sure had a big help on removing the changeling threat." He said. "Yeah, and we have to make sure they don't like, go back in time or something crazy like that would ever happen." Colgate said followed by Dr. Whooves giving her a stern look.
Once most of the changelings were gone, Cadence and Shining Armor were re-united. They put their horns together and began using their own magic to defeat Queen Chrysalis. She got blown away with the rest of her changeling army. It was now Dr. Whooves' time. The three went back out and went straight into the TARDIS. They used it to follow where the changelings were being sent. Eventually, they stopped getting thrown back and all fell. They seemed to be in a changeling colony. Dr. Whooves somehow knew exactly where everything was here. So did Colgate. Derpy just followed them, in fear. Dr. Whooves went straight for Queen Chrysalis and she moaned at the sight of another pony.
"I've had enough of you ponies. What more do you want? You already defeated me." Queen Chrysalis said. "Yes, and we're here to make sure you don't come back. But we're on friendly terms. Please come with me." Dr. Whooves said. Dr. Whooves led Queen Chrysalis to a closed up hut and told both Colgate and Derpy to wait outside. Queen Chrysalis and Dr. Whooves sat down face to face.
Dr. Whooves began talking "Make sure you don't come back? Phooey. I need you and you need me and just so that you know I'm telling the truth…" his body began changing. He changed from brown to black. He grew very long horn. Holes started appearing in his hooves. Queen Chrysalis looked at him, or what was actually more appropriate, her. She thought maybe there was some sort of mirror. Changelings couldn't change into other changelings so she knew it wasn't some changeling from her army. It was no mistake. Queen Chrysalis was looking at none other than herself.