This story came from an idea I was thinking of a few months ago, when I was searching the Doctor Who/Pokémon crossovers in the website and discovered how few PMD stories there were involving the Doctor and any of his companions. The summary is as follows:

After being attacked by a mysterious shadow in the TARDIS, the Doctor wakes up to find he's been turned into a Pokémon, he's lost his memory, and he's stranded in the world of Pokémon Mystery Dungeons. While he befriends the main Exploration team, the Legendary Beings gather the most powerful Psychic Pokémon to help fight an unknown force on their world and to help the Doctor recover his memories. Their plan – to bring some of his most loyal companions to their world to find his missing possessions, recover the TARDIS and locate the amnesiac Time Lord in time to save their world…

Time placement: Between "Planet of the Dead" and "The Waters of Mars"

Disclaimer: I do not own Doctor Who or Pokémon; they belong to their respective companies, so there.

So without further ado, let the story begin!

Prologue

Many years ago, the peace of the Pokémon world was rocked when two Pokémon, one of them formerly a human, arrived from the future to stop the Temporal Tower from collapsing and thus save their world from eternal darkness. They joined forces with the Pokémon Explorers' Club and formed an Exploration team. Calling themselves Team PokéHeroes, they were able to prevent the disaster and thus save the world. Through a series of events, Team PokéHeroes discovered the whole plan had been devised by the Dark Pokémon, Darkrai. They managed to defeat him and with his last strength, he disappeared from their sight. Peace was restored and Team PokéHeroes became the most famous Pokémon Exploration Team ever known. All was well, until one day….

The depths of space were quiet and still. The stars were shining brighter than the largest school of Chinchou in the seas. The moon shone its beams down on the planet below, bathing it in a silvery glow.

Then, almost from nowhere, a large pink dragon-like creature appeared in the cosmos. This was Palkia, the Legendary Pokémon of space. With a roar that shook the heavens, he soared through space faster than a Pidgeot. The pearls on his shoulders twinkled in the moonlight as he observed the blackness of space that surrounded the Pokémon world. With a satisfied nod, the mighty Spatial Pokémon prepared to return to his dimension.

Suddenly, a loud whooshing roar reached Palkia's ears. He turned to look and spotted a massive meteor shower approaching the planet below. He did a double-take and looked again. No, those weren't meteors. They looked too shiny, like the coat of a Magnezone. He flew in for a closer look.

At that moment, one of the meteor things spun round and made straight for Palkia! Quickly, the Dragon Pokémon soared over it, but it turned round and followed him. Realizing he couldn't escape, Palkia opened his mouth and fired a Hyper Beam at the meteor.

KABOOOOOMMM! The attack hit dead on target, smoke billowing over it. Palkia growled in victory. But then the meteor flew out of the smoke, seemingly unharmed.

"What the…? How was that possible?"the Spatial Pokémon snarled to himself. "Maybe Spatial Rend will destroy this thing…"

But just as he began to prepare the attack, the meteor opened up and a strange black shadow with thick arms burst out towards Palkia. With a roar of anger, he fired his attack, a wave of spatial energy zooming towards the shadow. But somehow, the shadow absorbed the energy into itself and kept going. Palkia tried to get away, but the shadow was too quick and it grabbed the Dragon in a powerful embrace. Palkia gasped; his mind felt like it was burning from the inside out.

The last thing the Legendary Pokémon saw before the darkness overwhelming his senses was the open doorway of the meteor and some strange black shapes, each with a glowing centre, looking out. And a mysterious voice saying, "This, my people, is only the beginning…"

Deep in the Time Vortex, a small blue box span and swirled, pausing momentarily to get its bearings before getting caught in the currents of time and space once more.

Inside, the Doctor pranced around the control console, twisting dials and pulling levers. "Come on, come on," he muttered to himself, although mostly to the TARDIS, "if you keep acting up like this, we'll never get to Barcelona. The Annual No-nosed Dog Show is coming on and I'll-"

Suddenly, the TARDIS was smashed sideways as if it was hit by a giant, and the Doctor was flung backwards into the passenger seat. Recovering quickly, he jumped up and switched on the scanner screen. At first, all he saw was the Vortex, its blue currents swirling like the inside of a tornado. Then he spotted a strange shadow zooming closer to the TARDIS.

The Doctor gaped incredulously, running his hand through his hair. "That's impossible!"

BOOOMM! The TARDIS was hit again, but this time, the Time Lord managed to grab on the console for balance and looked on the screen again. This time, he caught a proper glimpse of the shadow as it flew away. It looked like a large bluish dinosaur, with a massive sail of spikes on its back. Its body glowed with blue stripes along its sides and on its chest was a large chest plate, in which a large diamond sparkled.

The creature turned back towards the time vessel and the Doctor noticed something very wrong. There was something on its back, something dark with thick arms and a glowing pink centre. It crawled onto the beast's front, completely covering the chest plate and diamond, and then wrapped its arms around the neck. The creature let out a roar of agony as it smashed into the TARDIS and flew away.

"Oh no, you don't," the Doctor cried as he altered his ship's flight. Within seconds, the TARDIS was following the beast out of the Time Vortex and towards a distant planet.

Soon the beast crashed down in the middle of a forest, still crying out in pain, but not loud enough to drown out the whooshing, grating noise of a blue box appearing nearby. Inside the Doctor could only watch in horror as the cries faded and, moments later, the beast stood to its feet and let out an earth-trembling roar, its eyes glowing red and stripes now a deep purple.

The Doctor's eyes narrowed as he stared at the form on the beast's chest. "I know what you are," he growled. "And I'll stop whatever you're doing before it's too late…"

"It's already too late, Time Lord," a sinister voice hissed.

The Doctor whirled around to find a shadow standing inside the TARDIS with him. It was slightly shorter than a man, with wing-like appendages on its back and glowing blue eyes.

"Who or what are you," the Doctor snapped, "and how did you get in my ship?"

"It doesn't matter," the shadow sniggered as it started forming a ball of dark energy in its hands. "You can't stop my masters' plans, and this 'ship' of yours now belongs to them. As for you, you're no longer necessary, so now this world can be your home."

And with that, it launched the energy ball straight at the Doctor. Before he could react, he felt it strike and crashed to the floor with a cry. He felt something strange happen to his body, like it was changing. Was this it? He thought, Am I about to regenerate? Am I…

Then, as a villainous laugh filled the TARDIS, everything went black…

Wow, first chapter finished. So which Pokémon do you think the Doctor will become? I've already got an idea, but I might change it if I like your ideas. Note: they must be from PMD: Explorers of Time/Darkness/The Sky.

See you round.