Here, have some extra scenes. I liked ending the story where it was, and I don't plan on fleshing these out. Just a look at how things play out when the Doctor isn't the only remaining Time Lord, but the other is busy with a scientifically interesting town and a boyfriend. Enjoy!
When Harold Saxon brought the Toclafane to subdue Earth, Night Vale certainly handled it best. During the year she walked the Earth, Martha Jones found her only safe haven in the desert town. The deadly spheres had been no match for angels and Hooded Figures. Had anyone turned spy, the Sherriff's Secret Police was listening too closely for them to be one long.
Cecil's radio show could not be picked up by anyone on the Valiant, so he had Martha as a guest one day, and she shared her story of the Doctor with the town that way, adding in his involvement in the rescue of Carlos.
When the Master died and time rewound itself back a year, the Doctor went back to his TARDIS and found a message from the Scientist.
Everyone in town remembers. I have several hypotheses for why this is; need further data.
Just after he sent off what information he had, the TARDIS was hit by a large space-replica of the Titanic.
DW/WTNV
Carlos' TARDIS was a new, experimental model that could be operated by a single pilot. For a while, it had been disguised as an extra, unused closet in his lab. After showing it to Cecil, he had relocated it to their home.
One day, while teaching Cecil how to fly his TARDIS, a message arrived.
Went with my companion Donna to the Library that is an entire planet. I now understand, a little, Cecil's aversion to libraries.
Naturally, when the Doctor next dropped by with Donna, they demanded the whole story.
WTNV/DW
There were planets in the sky, Daleks were either killing people or rounding them up in the streets, and their only hope of contacting the Doctor wasn't working. Despite the efforts of Torchwood and Mr. Smith, they couldn't make the signal strong enough.
There was a sudden burst of static, and then out of their speakers came a voice Martha was very familiar with.
"The sky is now mostly void, partially planets. A call for help goes out, but will it reach its recipient? Welcome to the Medusa Cascade."
The exclamations from everyone, including Sarah Jane's "What on-" and Harriet Jones' "How did he get on the Subwave Network, it's completely secure-" almost drowned out the theme music. Martha shouted "It's okay, he's a friend!" before Cecil started talking again.
"Hello, listeners. My boyfriend, Carlos, wonderful and imperfect, has a message for our friend Martha Jones, so I'll turn the microphone over to him."
"Martha!" Carlos' voice was a welcome relief, in her opinion. "Hang on, I almost have visual…" a fifth video box popped up in the center of the screen, showing Carlos and Cecil in the Scientist's TARDIS. "There! Hello, Martha, Martha's friends. Listen, I'm sure you know your plan isn't working. It's a great plan and I would love to see what you're manipulating the Rift with, but the entire Medusa Cascade is one second out of sync with the rest of the universe. To get the signal out, you have to amplify it through space and time."
"And how are we supposed to do that?" Jack interrupted. "We don't have a TARDIS!"
"But I do," said Carlos. "The Scientist, Time Lord, school friend of the Doctor's, nice to meet you." He held up a hand to silence the incredulous cries. "Now, I just need to…"
Later
"The Doctor to the Scientist, can you hear me?"
"Loud and clear, Doctor."
"Lovely to know you're still alive. How's the town?
"Honestly, the Daleks are much worse off, having invaded on Street Cleaning Day. What do you need?"
"I have to tow the Earth back into position. Does your TARDIS have enough energy to help out?"
"Scientifically speaking, yes."
"Multo bene! Connect with Mr. Smith, he'll anchor you to the Rift."
"Got it. Hang on tight, Cecil!"
"If Cecil decided to "hang on" by circling his arms around his boyfriend's waist, well, Carlos didn't mind.
DW/WTNV
"Come on, Ponds, we haven't got all day! If we don't get there soon, dinner will be cold! And have you ever had cold wheat-free pasta, it is not pleasant, let me tell you."
"All right, all right," Amy replied as she finally emerged with Rory in tow. "We're ready! Since when are you in a hurry to get somewhere?"
"Cold wheat-free pasta!" the Doctor reminded her. He went to the door, stopped, and spun around, clapping his hands. "Right, before we disembark, some ground rules. First off, do not, under any circumstances, acknowledge the Hooded Figures. Two, angels are everywhere but legally do not exist, so if you see one it's best to ignore it. Third, neither of you have bread in your pockets, do you?"
"Why would we have bread in our pockets?" Rory questioned.
"Because I told you we were having wheat-free pasta," the Doctor replied, "and you might have been tempted to bring some dangerous contraband with you."
"Bread is dangerous contraband? What kind of place is this, Doctor?" Amy asked.
"Oh, just a small desert town, now come along!"
Cecil answered the door at the Doctor's eager knock. He only blinked before smiling and saying "Hello again, Doctor. Is that a new face?"
"It sure is, Cecil, and I've got new companions too! Amy, Rory, this is my friend Cecil Palmer. Cecil, meet Amy and Rory Pond."
"Williams," Rory muttered, but he was ignored. Cecil shook hands with the couple.
"Pleased to meet you." The radio host said. "Come in, you're just in time; Carlos is almost finished making the semolina pasta."
A few minutes after they settled into the living room, the Scientist came in to announce dinner was ready. Of course he, too, noticed the new form, but the Doctor sprang to his feet to greet him before he could comment.
"Hello, Scientist, good to see you again. Thanks for having us for dinner. Meet my companions, Amy and Rory! Amy, Rory, this is Carlos, but among Time Lords he's the Scientist! You remember what I told you about the Corsair's tattoo?" Of course they did, their adventure with House had been two days ago. "Well, the Scientist, in every regeneration, has always had the most amazing, perfect hair."
"Oh thank the Glow Cloud," Cecil muttered, relieved.
Much later, when the Doctor and the Ponds had returned to their travels, Amy voiced a thought she'd been having.
"Doctor, does the Scientist have a TARDIS too?"
"Of course!"
"But," Rory said, "You told House that this one was the last in the whole universe; that was the whole reason he took it over!"
The Doctor didn't give them a straight answer that they believed, but he didn't need to. All of his companions who had met Cecil and Carlos would eventually notice that he didn't mention them at all to anyone who wasn't traveling with him long-term. He would still spin a tale of being the last of his kind, and excuse it as an old habit. However, anyone who knew him knew that it was actually the only way he knew to protect the only other member of his race left. Losing the Master, even if he had been an enemy, had nearly destroyed him, and to lose his friend would be so much worse.
WTNV/DW
The Doctor was always full of excited energy, but when he exited his TARDIS on this particular visit to his friends, he was positively overflowing with it. He skipped over greeting Cecil and Carlos, instead making a beeline for the latter and gripping his shoulders. Giving him a shake, he said "Scientist! Oh, but you will not believe this! I'd forgotten until now, but I didn't destroy Gallifrey!"
After so long in Night Vale, not much could surprise Carlos, but this news left him understandably slack-jawed. "What?" he asked. "But, Doctor, I've been to where Gallifrey was, and it isn't there. If you didn't destroy it, then what happened to it?"
"That's the beauty of it," the Doctor replied, "I place the whole planet in stasis!"
The Scientist's mind whirled. Scientifically speaking, to place an entire planet into stasis wasn't impossible, but… "The calculations for that would be astronomical!" he said, gripping the Doctor's arms as his own excitement grew. "They would take-"
"Thousands of years, yes." The Doctor finished.
During all this, Clara had sidled up to Cecil and introduced herself. "Hello, I'm Clara. I'm with the mad one in the bow tie."
"Cecil Palmer." He shook her hand. "That is my husband, Carlos the Scientist, or just the Scientist, as the Time Lords know him."
By now, the two Time Lords had grown so excited that they started jumping up and down, talking a million miles an hour and voices growing in volume.
"Does this happen a lot?" Clara asked Cecil.
"The Doctor, I don't know, but Carlos gets excited very easily, especially about science. It's one of the things I love about him."
Seeing as Carlos and the Doctor showed no signs of letting up anytime soon-the Doctor was telling of his adventures with two earlier versions of himself while the Scientist interrupted often with science questions-Cecil invited Clara to the radio station to meek Khoshek and his kittens. The four of them later had a lovely dinner at Gino's Italian Dining Experience before the Doctor and Clara went off again.
All finished with these! That last one is partly thanks to my friend RasenganFin. He asked me about Carlos and the Doctor jumping up and down like excited kids when the Doctor revealed that Gallifrey wasn't gone. I concluded that Carlos is indeed that much of a dork.
Once again, thanks for reading, and please review!