The Doctor entered the Zygon ship, and walked to the bridge. The commander approached The Doctor. "We can still infect you, Doctor." He threatened.
"Oh, don't be so daft." The Doctor said. "It's over. As soon as the cure was injected into the atmosphere, everyone on Earth was cured. And, once I opened those doors, the cure was released into the ship. All of you are cured. Every atom, every molecule, of the virus has been erased. There is no more virus for you to infect people with."
"We're the last Zygons in existence, Doctor," The commander said, "and you've sentenced us to death."
"No I haven't." The Doctor argued, "There is a way. I can take you to an uninhabited world, much like Zygor. You can start again. You don't need to conquer a world to live on it."
"Yes we do, Doctor!" The commander shouted. "We have evolved too much to live on a desolate world. We require a world with advanced technology!"
"I'm offering you a chance to live!" The Doctor shouted.
"Well, we do not accept!" The commander shouted. He walked over to a console and pressed several switches.
A voice rang out throughout the ship: "Self destruct initiated. Thirty seconds to self destruct."
"What are you doing?!" The Doctor shouted.
"If the Zygons are to be extinct, then so will the Time-Lords!" The Zygon commander shouted. The Doctor ran through the ship to the exit. He ran out, and less than five seconds later, the Zygon ship exploded.
The Doctor looked at the wreckage thinking about how he had just caused another species to extinction. And he had even more weight on his conscience.
The Doctor arrived at the TARDIS. Twilight and Sunset were sitting outside it, talking. "So, back to Equestria." The Doctor said, opening the doors.
"Actually," Twilight began. The Doctor turned around. "I was hoping to see some things here. After all, I've been to a lot of past Equestria, and I'd like to see something new. I was hoping to see some of this universe."
"If that's what you'd like." The Doctor said, and walked into the TARDIS. Twilight followed him, and Sunset followed her.
The Doctor took of his trench coat, and tossed it onto one of the structural supports. He began to press buttons on the console, and then turned around. "Yes?" He asked Sunset, who was standing at the entrance.
"I was wondering if I could come with you guys." Sunset said. "I mean, I'd understand if you say no, since I've done some pretty bad things, but I was hoping I could come with you."
"Sunset," The Doctor began, "We've all done terrible things in our lives, myself included. To stop a war, I destroyed my home planet, and all my people. I am alone in the universe, the last Time-Lord. If everyone didn't trust be for that, then I wouldn't have a purpose in life. I trust you, and I hope that you trust me. Of course you can come."
"Really?" Sunset asked, excitedly.
"Really." The Doctor confirmed.
"Oh, thank you!" Sunset shouted.
The Doctor walked around the console. "So, have either of you ever been to New York?"
"No." Twilight and Sunset said.
"All right then, New York. Let's say twenty thirty-three." The Doctor pulled a lever on the console, and the TARDIS disappeared into the time vortex.