Derpy Hooves arrives at Dr. Whooves house after finding a note with the rest of her mail telling her to go there. After introducing herself, Dr. Whooves and Colgate let her in and do the same but in a very mysterious fashion. They explain to her that they're on a top secret mission for Princess Celestia. They want Derpy to help them on their mission but they need to ask for Princess Celestia's permission first.
The three make their way to Princess Celestia in Canterlot. After asking for her permission, she gives it to them, choosing to have faith in her subjects. She explains that their mission is to make sure the changeling threat is gone. Dr. Whooves, Colgate, and Derpy head back to his house and he begins to explain more. The only way to make sure the changeling threat is gone is to follow it from it's source. The source was when they attacked the castle during the Royal Canterlot Wedding. Because of this, they would have to go back in time so Dr. Whooves reveals the TARDIS to Derpy. After an annoyingly painful time trying to explain what the TARDIS was to Derpy, she finally ends up grasping the concept and heading inside of it with the others.

Dr. Whooves then takes the TARDIS to the wedding day and explains to Derpy that she can not tell anypony about the events of the future as it could result in a time paradox causing the very notion of existence to cease to exist. The three get closer to the castle and hear Princess Cadence (who they know to be Queen Chrysalis) singing the first part of This Day Aria. The changelings wouldn't be exposed for some time so they would have to wait, all while not exposing their identities of the future. After waiting awhile, the Queen Chrysalis and the changelings get defeated by Shining Armor and the real Princess Cadence's power. Now seeing their chance, the three head back into the TARDIS and follow them into a changeling colony. After they arrive, Queen Chrysalis looks unhappy to see ponies in her territory but figures she can't do anything about it now. Dr. Whooves makes Colgate and Derpy wait outside while he and Queen Chrysalis head inside a hut. He begins talking to her and his body begins changing, only to reveal that he is actually Queen Chrysalis from the future!

After some explaining, the past Queen Chrysalis joins with the future Queen Chrysalis. Colgate turns out to be one of the changelings from the army and brings Derpy to the dungeon. The two Chrysalises head into the TARDIS and go back to the time when the future Chrysalis first arrived. They managed to rope that Chrysalis in after making that Colgate take that Derpy to the dungeon in the changeling colony as well. As Shining Armor and Cadence were getting ready to defeat the changelings, the three Chrysalises burst in, scaring them for a second causing the spell to fail. Now, with four Chrysalises, they know that even Shining Armor and Cadence's powers can defeat them. The Chrysalises lit up their horns and so did Shining Armor and Cadence. Their power wasn't enough and the Chrysalieses won. All the ponies were laying on the floor.

Meanwhile, right after Colgate took Derpy to the dungeon, someone else appeared inside. It turns out to also be Derpy Hooves. The changeling colony had a protective time bubble on it so that things can go through it but not time. Any time alterations would not effect what happened inside the bubble. The Derpy who got thrown in by the three Chrysalis was there along with the first Derpy. They plotted hwo to escape and did. There was nothing two Derpy Hooves from parallel universes couldn't acomplish. The two ran to where they left the TARDIS and went inside. Now, out of the bubble, things from another universe couldn't exist anymore. Only the Derpy from the alternate universe could. The main Derpy faded away from existence and made sure the other Derpy would eat lots and lots of muffins. Now, this Derpy Hooves would have to defeat the Queen Chrysalises on her own.

The TARDIS suddenly headed for present time on it's own. When she stepped out of it, she was in Dr. Whooves' house again and heard noises from the closet. She found out that these were the real Dr. Whooves and Colgate and that Queen Chrysalis had thrown them in there earlier. They weren't affected by the timeline alteration, though, because his house also had a time bubble. Derpy looked outside and noticed that all the ponies were being used as slaves for the changelings. Dr. Whooves explains that the TARDIS also had it's own time bubble and that's why she wasn't affected either. He goes on a huge speech explaining what she must do to defeat them which is basically to go back in time, use the time bubble as an time explosion, and that should fix any errors made in time. The three risks with that is that she would have to do it before any time jumps were made which means before the Chrysalis Cadence was singing This Day Aria, she would have to go back to the present before the time bubble exploaded or else she would forget all her memory, and once back in the present, she would have to defeat Chrysalis and not get fooled by her again while in Dr. Whooves' form. Dr. Whooves then pulls out a recording device and tells her that he just recorded his whole speech. After time was fixed, he wouldn't remember anything so she would have to give him the recording to listen to. That's when changelings burst in his house and started using their magic against Dr. Whooves and colgate. Derpy ran for the TARDIS with the recording. He heard their screaming of pain and then complete silence, followed by a splatter of red liquid on a window of the TARDIS which she assumes to be their blood and begins crying. Banging on the door by the changelings scare her into place and takes the TARDIS back in time once more.

Once she was at the wedding day again, she realized that Dr. Whooves never told her how to detonate the TARDIS' time bubble. On her own, she comes up with an idea of creating a time paradox within a time bubble which might be enough to make it implode on itself followed by exploding. She finds her own past self and blindfolds her so that no time paradoxes would occur outside of the TARDIS. Otherwise, as Dr. Whooves said, it would result it everything ceasing to exist. Once inside, she takes the blindfold off and talks to her telling her not to do exactly what she was doing now, thus causing a time paradox. The bubble couldn't contain a universe wide paradox and exploded. She sent the TARDIS for the future at the exact same time and fell unconscious. Hopefully she would remember everything when she awoke. If it hadn't worked, even the recording might be lost. Luckily, she awoke all of a sudden but she somehow wasn't in the TARDIS anymore. Instead, she was flying and had a note in her hand to tell her to go to Dr. Whooves house. She had all of her memories and knew exactly what was going on now. She went straight for the house, helped Dr. Whooves and Colgate escape and then tackled Chrysalis in her Dr. Whooves form. She, Colgate, and Dr. Whooves then entered the TARDIS and headed for the Princess' castle. She played the recording for him and then he believed her entirely. They went to talk with Princess Celestia who told them they would need to find the Mane 6 if they had a chance of defeating Chrysalis. They went straight for Twilight's house first and she let them in.

The ponies then went looking for the other 5 of the mane 6. The first they found was Rarity and now she was helping them look. Meanwhile, Spike was still at Twilight's house. He opened the door for who he thought to be Rarity but was actually Chrysalis, as he later found out after she trapped him in Rarity's boutique. She then transformed into Spike and waited for them at Twilight's house. After all the ponies found each other, they headed back to Twilight's house, the location of which Princess Celestia said she would meet them. Once inside, Chrysalis in Spike's form trapped the ponies inside the house and made her way outside to the TARDIS. It wasn't hard for the ponies to escape because they had magic to teleport. They now surrounded the TARDIS and wouldn't let her in. Princess Celestia, Princess Luna, Princess Cadence, and Shinging Armor arrived who Twilight immediately hugged because she hadn't seen them since the wedding now that they were on their honeymoon. They all went inside the TARDIS and used their powers. The power of love, the Princess' power, and the Elements of Harmony. From inside, the power created a chain reaction which cased the time bubble to explode once more except this time it worked as a barrier for the changeling colony. The changelings were now trapped in their colony like a fish in a fish bowl and they had no way out. They had succeeded in finally defeating Queen Chrysalis. After thanking each other, the ponies went back to their homes and Dr. Whooves, Colgate, and Derpy headed back to his house.

Once there, Dr. Whooves told Derpy the full story about how at first he thought Princess Celestia was plotting something beyond the changelings and beyond Equestria. He thought she was planning a conspiracy but now knew he was wrong. He told her also about how he was recruited for Princess Celestia's mission. Afterward, they all went to Princess Celestia to officially make Derpy Hooves a part of their team. Princess Celestia frowned and apologized for what she was about to do but she couldn't have anybody know about anything that could possilby happen. She took out a pen that the three ponies looked into and Celestia used it to make them forget their memories - Men In Black style. She put them in the TARDIS and sent them back. What she didn't know was that Derpy had the recording device recording the entire time and Celestia might had soon be in for it. For now, however, everybody was safe and that was what was important. Even Celestia's secret was safe and if it were up to her, nopony would ever know it...

Meanwhile, as the ponies were partying at Sugar Cube Corner to celebrate Queen Chrysalis' defeat, Spike stayed in Rarity's boutique. Still trapped in the closet. With nopony to help him out.