"Please, Derpy Hooves, stay here." Dr. Whooves said, motioning Derpy to stay inside the TARDIS. The TARDIS went back to his house and the three of them went inside. "Now Derpy, I'm aware that you had to time jump. Please, tell me everything." Dr. Whooves said. After seeing Chrysalis being defeated for good, Derpy was sure that she could trust this Dr. Whooves. What were the odds of it being another trick? Derpy did just what he told her to do and told him everything. From the fake Dr. Whooves all the way to exploding time bubbles. Dr. Whooves was listening attentively the whole time. "So you went back and forth through times that much? And even had contact with yourself from a different timeline?" Dr. Whooves asked even though he already knew the answer. Derpy nodded. "That surely can't be good for a pony. Are you sure you're alright?" Dr. Whooves asked. Derpy nodded again. "Well, there is one very important thing about what you're telling me. When you first met Chrysalis, when she was in my form, most of what she told you was true." Dr. Whooves began.
"Princess Celestia was on a secret mission. She was trying to find out if the changeling threat was really gone but she didn't want to tell anypony. I thought she wasn't telling anypony because there was something beyond changelings. Possibly even beyond Equestria. I thought there was a conspiracy going on. I found out that I was wrong, however, that wasn't until after I did some snooping around with my pal Colgate. We used the TARDIS to figure out what Princess Celestia was planning and I didn't find anything conspiracy worthy. I eventually stopped snooping and decided to talk to her face to face." Dr. Whooves explained.
"Princess Celestia somehow knew I was snooping. She knew it even while I was bending the laws of time and space with the TARDIS. I don't know how nor do I think I'll ever know how but she knew. She also knew that she had no choice but to confess everything to me. She knew I would eventually find out regardless. When I went to speak to her she told me her plans about finding the changelings. At first I thought she was just hiding her true plans again but she then asked me to help. Both Colgate and I. Apparently she figured that with the TARDIS, we would have a much better chance at finding the changelings so she chose us." Now Dr. Whooves' face began to look grim.
"However, if he chose to accept her mission, we would have to keep it a complete secret. This is why Princess Celestia wasn't sure about accepting you when the fake Colgate and I were asking you to join our team. I wouldn't have expected it but she somehow accepted. She must have a lot of trust in us. Anyway, my point is that now you know all about it. Normally, in cases like these, we would go back in time and stop you from ever finding out about any of this. Problem with that is that you played the key role in all of this. Without you, Chrysalis could have found some other pony to help her out and you would have never been able to stop her. You're the reason everything was fixed. You're the reason that we're all alive here speaking right now. We can't erase your memory and change time. You're forcefully part of our team now. Unfortunately, this means you can't tell anypony about anything anymore. The only ponies you can talk to about time travel, space travel, and the TARDIS right now is Princess Celestia, Colgate, and I. You can't even tell Princess Luna. She has no idea about Celestia's plans. You can talk about anything else. Even the changelings and Queen Chrysalis. Just nothing specifically about her mission. Got it?" Dr. Whooves asked.
Dr. Whooves had a habit of talking a lot and everything going above Derpy's head although she understood most of it and nodded. "Very well. Welcome aboard then." Colgate said. "The last thing we need to do is update with the Princess." said Dr. Whooves and they all got into the TARDIS once more and headed for Princess Celestia's castle.
Once inside, they went straight to Princess Celestia's chamber. She stepped down to be right next to them. "I am aware that Derpy now knows our secret." she said and Dr. Whooves nodded. "Well, I have to apologize. I hate doing things like this to my own subjects. Just trust me when I saw I love you all dearly. However, I have no use for you anymore. You can have no recollection of this." Celestia continued to say. "We have already told you, we can't go back in time and stop us from knowing about it. That will change everything and the changelings will be in power." Dr. Whooves said. "Who said anything about time travel?" Celestia argued. She pulled out a pen. "Do you see this? It's a really cool looking pen, is it not?" she asked. Derpy was in awe. If was really cool and futuristic looking. All three of them were staring at it. Princess Celestia closed her eyes and pressed the end of it. A bright red flash of light came out of it and blinded the three ponies for a few minutes. They were practically unconscious.
Princess Celestia grabbed them and put them in the TARDIS. She set it to go back to Dr. Whooves house. It soon disappeared and Celestia was alone once more. She sighed. "I hate doing that to my friends. I just can never let them learn about my true motives. It would become a great disaster..." she said as she walked back up to her throne. There was, however, one thing that the Princess wasn't counting on. After Derpy had finished playing the recording for Dr. Whooves much earlier, instead of pressing the off button, she hit the record button. The recorder had been recording everything from talking to Dr. Whooves to talking to Princess Celestia. They had forgotten all their memories about time travel but they would soon recover some of them after finding the recorder. Given the fact that it was Derpy who had it, it could have been a very long time before they did. Either way, everything was now calm in Equestria with no threats from anypony. Even Celestia didn't want to harm anypony, she just had a very big secret. Unfortunately, nopony would ever know...
Meanwhile in Rarity's boutique...
"Hello! Is there anypony there!" Spike said pounding on the closet door. "Rarity? Are you here?" Spike continued with no response. The mane six were all celebrating Chrysalis' defeat at Sugar Cube Corner. "Awww..." Spike moaned, sitting down, realizing there still wasn't anypony around.