For a while things were, in a way, perfect for the residents of the TARDIS.
The Doctor and Rose were as strong as ever, and they adventured around with Rory and Amy, rewrote time once or twice and saved a lot of people. Many died, but there was a significant majority who lived. And The Doctor could deal with that, because with Rose he knew that he could face anything. And that's why everything was about as perfect as you could get, by nearly dying every day.
But then The Doctor started getting all of these warnings, about the silence. And he wasn't sure what they were but they just kept hearing about them everywhere. Donna's words, 'silence will fall' kept ringing in his ears. And then they met them, the silence. The Doctor, Rose, Amy, Rory, River and Jack ran around space 1969 sorting them out and destroying them and they managed to solve the problem, but something else happened.
Something that The Doctor was pretty sure he wasn't supposed to have overheard was said.
Between Rose and Jack.
Flashback
It was coming for them, the little girl in the spacesuit and Rose was pretty sure that her and Jack were possibly not going to make it, and she would have to regenerate, which she wasn't sure she could even do. Especially not in her condition. She had to tell someone, just in case they were her last words, she had to say them.
She gripped onto Canton's firearm that he had given her and stood up, and then everything seemed to go in slow motion. She turned to Jack, her best friend who was probably the only person other than The Doctor that she could tell about this. She had to tell him. He would tell her.
"Jack." She said, standing up and aiming the gun. Jack turned his head to face her, and stood next to her. He noticed the tears streaming down her face, and then didn't hear anything but her cry of 'I'm pregnant' before a gunshot rang out and barely missed the child's face.
And The Doctor suddenly ran out from his hiding spot behind some boxes, and had to pretend that he didn't overhear what had just been said.
When they got back, the doctor just had to find out if it was true. He had heard Rose telling Jack afterwards in the TARDIS that it was a 'false alarm' but he had to be sure. This could possibly be the restarting of his race, developing and he would have to be sure. So when he was sure nobody was looking, he scanned her. And he looked up at the monitor, holding his breath. And then he watched as the scan flickered from positive to negative and almost gasped, before remembering Rose was barely a few feet away from him.
"Whatcha looking at doctor?" she asked him, after about ten seconds of him just staring at the monitor.
"Oh erm, nothing. Time we got you to bed yeah?" he said, giving her a soft smile and turning the monitor off.
"Oh doctor if I didn't know better I'd say you were trying to get me inside your bedroom" Rose said with a wink
"Well Rose for once I'm not, after the adventure we've just had, even I could do with a kip, and I know you're a lot more knackered than you let on." He said, before snaking his arm around her waist, and walking off with her down the corridor.
"You know me so well." She said, leaning her head into his chest as they walked.
"Yeah, and you know me better than anyone. You'd tell me anything, right?" he asked, stopping outside their door and actually looking at her in the eyes
"Of course." She said back to him, and she looked so convincing that The Doctor almost believed her.
-Line Break-
From that day on, Rose seemed normal. She acted normally, spoke normally, and was pretty much just Rose.
But The Doctor just knew there was something wrong. He would often pace the corridors at night thinking about it whilst she was asleep. He knew that Rose wouldn't tell Jack that she was pregnant unless she was absolutely completely sure. So why wasn't she showing any vital signs of pregnancy?
He kept on scanning and scanning her, but the results were inconclusive. And then there was the fact that Rose kept seeing things. She told him that she kept seeing a hatch, open up in front of her when they were in random places, and there would be a woman on the other side. Who would say things like 'Yes she's fine, just dreaming' or 'no, she isn't ready yet' and it seriously unnerved her. After it had happened more that twice she knew she had to tell him, and he said that he would look into it.
He acted a lot calmer than he felt. He was pretty sure that something or someone had taken her, and was projecting almost a signal of her here, with him and that worried him. And he had to trace the signal, which was almost impossible. He didn't tell anyone else, especially not Rose because he didn't want whoever or whatever it was on the other side, hearing that he had maybe worked out there plan.
This had to be done in secret, and he had a feeling that it was going to take a very long time.
