Outside Town Hall, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.

The gravity of Applejack's words hit Twilight like a brick. She felt as though she was about to upchuck her entire stomach. She'd been missing for five months! While she was off traveling with the Doctor, fighting strange enemies, and helping ponies throughout time and space her friends were worrying and looking for her for five whole months!

"It can't be," Twilight choked.

"It's true!" said Pinkie Pie. "I remember the day exactly! It was June 19. That was exactly five months ago!"

"That's when the metal thingy attacked the town and that strange stallion showed up!" said Rainbow Dash.

"Don't worry, Twilight! We'll make sure he doesn't get away with whatever he did to you!" Spike said. His face was full of rage and Twilight could see five months of sadness hiding away behind those eyes. Then she realized what was happening. Everypony thought that the Doctor had kidnapped her!

"Wait!" she said. "It's not what it looks like! You see-"

"Twilight!" called a familiar voice. Twilight groaned as she looked back to see the Doctor running towards her. "We've arrived a tad bit late!"

"A tad?! You call five months a tad bit late?!"

"Well-"

"There he is!" Rainbow Dash snapped. "There's the pony that kidnapped Twilight!"

"What?"

"Get him!" cried the crowd.

"WHAT?!"

"WAIT!" Twilight cried. But her cries proved fruitless as the crowd of ponies charged at the Doctor. The Doctor turned and ran like he had never run before.

The Doctor could hear the ponies screaming behind him. He didn't dare look back. He knew that would lead to him getting caught and kicked into a pulp. He made a quick turn and ran for the library. The TARDIS was his last safe haven. Normally he would try to talk sense into them but it's hard to talk sense to a wall of ponies, pegasi, and unicorns charging at you with the full force of their bodies. The pegasus known as Rainbow Dash was certainly giving him the shivers. He remembered meeting her in Sugar Cube Corner when the Dalek had appeared. Even though he had known her for a couple minutes at max, he knew that she was not a pony that you wanted to tick off. Sadly, he had managed to tick her off by making her friend disappear off the face of the planet for five months. Obviously, that was a big mistake.

"Come back here!" snapped Rainbow Dash as she flew towards the Doctor. The Doctor dodged her barrel roll and made his way down a nearby street. He turned back just in time to feel a pair of hooves grab him and pull him into a nearby alleyway. A hoof covered his mouth and he watched as the crowd of ponies rushed past the alleyway entrance. "Where the hay did he go off to?!"

It wasn't until the sound of the crowd had disappeared that the hoof wrapped around the Doctor's mouth moved aside. The Doctor turned to find himself staring into a pair of bright, yellow eyes. The eyes randomly pointed off in awkward directions for a few seconds before returning to a normal state. It wasn't until the Doctor saw the gray coat, the wings, and the blonde mane that he realized who had saved him.

"You've got a lot of explaining to do, Mr. Doctor!" snapped Derpy Hooves.

Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.

This was a disaster. Plain and simple. Not only had she returned five months late but now the Doctor, the stallion who saved Ponyville as well as many other places throughout time and space, was now being accused of kidnapping her. She opened the door and trudged inside the library. Owlowiscious flew down from upstairs and hooted with delight at the return of his owner.

"Hi, Owlowiscious," she sighed. She looked around the library and noticed just how cleaned up it was. It was surprisingly clean for a library that hadn't been organized regularly in five months. "It's certainly clean in here."

"You can thank Spike for that," said a small voice. Twilight turned to see Fluttershy standing in the doorway.

"Fluttershy. I thought you went with the others."

"I don't like mobs. They frighten me."

"No surprise there. Listen, Fluttershy. You've got to help me tell the others that this is just one huge misunderstanding! The Doctor did not kidnap me!"

Fluttershy fell silent. Twilight noticed that she was staring at the TARDIS, which was still parked in the middle of the library.

"Spike told me about that blue box. Is it true that it's his ship?" she asked. Twilight nodded as Fluttershy approached the TARDIS. "What happened, Twilight? Where did you go?"

"Do you remember what happened five months ago? The Dalek attack?" Twilight asked.

"What's a Dalek?"

"It's the creature that attacked Ponyville the day I went away with the Doctor."

"I never saw it. I was home alone all day with Angel."

"The Doctor and I defeated it. The Dalek, however, damaged the ship and it took us away."

"To where?"

"Other places in space...and time."

"Are you saying that you-"

"Traveled through time? Yes. That's exactly what I'm saying. We traveled 1000 years in the future, we visited a fort on another planet in 1899, we traveled to Canterlot in 987, and our last stop was Equestria 100 years prior to Princess Celestia's birth."

"That's...unbelievable."

"Tell me about it. So...Spike told you about the TARDIS?"

"That's what it's called? Well, yes. Spike and Princess Luna told us all about the Doctor and his mysterious arrival. From what we gathered, I guess it was only natural for us to assume that he had kidnapped you...or something worse had happened."

Twilight sighed. She thought about the last time she had seen Spike before heading off with the Doctor.

"I promise I'll come back! Don't I always keep my promises?" she had said. For her, it had been around a few days at max since that occurred. For Spike, it had been five months, nearly half a year. The thought made Twilight sick to her stomach. Twilight looked at Fluttershy and said, "Come on. I need you to help me calm down the others."

Fluttershy nodded and Owlowiscious flew back up to his perch. Twilight and Fluttershy then exited the library.

Home of Derpy Hooves, Ponyville, Equestria, Gaia, Autumn, 1002 C.E.

The Doctor sat awkwardly across from the gray pegasus. The hunting party had grown quiet and the Doctor was happy for that. He eagerly scarfed down the blueberry muffin that Derpy had given him as a snack.

"Thank you for the snack, and saving my rump back there. I really owe you one, Ms. Hooves," he said.

"Just call me Derpy, Mr. Doctor. That's what everypony else calls me," she replied.

"Only if you drop the Mr. bit. I prefer to just be called Doctor, thank you very much."

"Okay then!"

Derpy giggled as the Doctor took one last bite from his muffin. Once the muffin was gone, Derpy instantly began staring the Doctor down.

"Now let's cut to the chase! Did you or did you not kidnap Twilight Sparkle?" she asked.

"I did not kidnap her. Me taking her away was a complete accident. That damn Dalek is to blame. Screwing up my controls and damaging my TARDIS. Isn't that just inconsiderate?!" the Doctor replied.

"I guess."

"Do you believe me?"

"Actually, I do."

"That's good."

"Question. Do you happen to know a mare with a dark red coat, a purple mane, and blue eyes?"

"I actually do. Her name's Matilda."

"You can thank her for me believing you. She appeared to me on the day Twilight disappeared."

"Did she say anything?"

"She said that she knew me well and that I had an adventurous future waiting for me. I think it had something to do with you and Twilight."

"Tell me, Derpy. Do you know Twilight Sparkle and her friends well?"

"Not really. I'm just one of those background ponies. I don't talk to or know a lot of other ponies."

"This town seems pretty upset about Twilight disappearing."

"Well Twilight represents one of the Elements of Harmony and she's a pupil of Princess Celestia herself. She's a very well-known pony around town. Her disappearance has probably affected Princess Luna the most."

"How so?"

"When Princess Celestia came to Ponyville to learn about the details regarding Twilight's disappearance, Luna was the one to fill her in. She told Celestia about her interactions with you and Celestia didn't take kindly to that."

"What do you mean by that?"

"Celestia told Luna that she was foolish to leave Twilight, her star pupil, unprotected and allow her to get kidnapped by a strange stallion. Luna's had it rough the past five months."

"Well I plan on mending things as soon as possible. Once I manage to clear everything up."

"I hardly doubt a lot of the ponies in this town are going to listen to you, no offense. Rainbow Dash is going to be especially hard to move."

"No offense taken and I see what you mean. I just need to find Twilight and then we can establish a game plan."

"Okay. But we've got to be careful. Until we get things straightened out, you're public enemy #1."

"Got it."

The Doctor and Derpy made their way through the front door and out into the cold autumn air.

Zecora's House, Everfree Forest, Equestria, Gaia, Autumn, 1002 C.E.

Zecora the zebra was preparing a new batch of potions in her house when she heard a peculiar sound emanate from outside. She walked towards the door and poked her head out.

"Who is there, if I may ask? Perhaps a pony with another task?" she asked. The sounds stopped but a small light appeared off in the distance. Zecora instantly recognized the light as that of a fire and began making her way towards the source. "Careful, friend, that is not good, for a flame is no ally to wood!"

Zecora was so focused on reaching the source of the fire that she didn't notice the two, tall, dark figures approach her from behind. There was a swinging motion, Zecora felt a sharp pain rush through her skull, and she blacked out.