By giftedmunchkin

“What are you doing, though?” asked Donna.

“I told you,” said the Doctor, spinning a wheel on the TARDIS’ control panel, “I’m initiating a protocol that will adjust the wavelengths of the ambient levels within the TARDIS, interpolating the air around us.”

“But what does that mean?” asked Donna. She always got frustrated when he did this, running about the TARDIS flipping this switch and that dongle without explaining it. In response, he took a lever on the console and abruptly pulled it down. He grinned madly as “Under the Sea” started playing in the air.

“Tell me, Donna,” said the Doctor, as he began fiddling with some of the other controls, “have you ever been under the sea?”

“Once, yeah,” said Donna. “In Spain, I went scuba diving. Why?”

“Because, Donna Noble, I am about to take you to the first underwater colony on Earth – Atlantis!”

“Wait a minute,” said Donna, stopping the Doctor as he started to run out the door. “Naming an undersea colony after Atlantis? Doesn’t that seem like a bit of a bad idea?”

“I was on a spaceship named Titanic once, and it ended up perfectly fine.” He ran out the door, then a moment later stuck his head in again. “Well, I say fine, I mean okay. Well, I say okay, I mean three or four people lived.” He grinned again. “But I’m sure this will be nothing like that here. Come on, then!”

Naturally, things go wrong. It turns out it wasn’t a good idea to name an underwater sea base after a city that sunk into the ocean. It turns out that there’s something under the water that has been sleeping for many years. It’s been undisturbed for centuries, but the recent activity and heat in the area has woken it up, and it isn’t friendly.
An alien ship crash landed near where the Atlantis sea base was built centuries ago. Coral and rock has covered it up for the most part, leaving it safe from detection by human scans. But when an expedition to get some of this coral for observation goes awry, the base finds itself under attack by the alien monster. The Doctor and his companion(s) have to stop the monster or save the inhabitants of the colony before the glass walls come crashing down and they all drown.
Naturally, there are plenty of complications that would likely arise out of what was going on. Here are some that I can think of:

• The crew would try to attack the monster with missiles and other weaponry. Naturally, the Doctor would not approve, because the monster probably doesn’t even realize what it’s doing – it’s lost, and scared, and there are strange creatures trying to steal its ship (in truth, just getting coral), and it is just lashing out.
• One of the first portions of the base to be destroyed is obviously the most convenient way to get to the surface. Everyone will have to rush to the furthest transportation deck to make it home safely.
• Organizing an entire colony might be a bit challenge of its own – although, with the Doctor’s presence and the effect he tends to have on people, that might be less of a problem.
• Once they finally do make it to the ships, they have to outrun the monster to the surface.