Author Notes: SORRY! Been away for three weeks, and I didn't have time to update on the day I was at home since the chapter wasn't complete. I apologise profusely for this. Bit saddened now since Doctor Who has now finished in the UK, but I did thoroughly enjoy the series…enough of my chat and onto the story…so here you go, chapter four!

Note: This chapter takes place before the end of the last chapter, but instead of end being from Jack's point of view, this one is from the Doctor's point of view. Enjoy!

Four

Thankfully, Rose and Martha had made it back to the TARDIS way before the Doctor returned from his meeting with the Face of Boe so he was none the wiser. Mickey had already been told about Rose's pregnancy leaving only the Doctor in the dark. Rose had still not decided whether to inform him of his impending child, but when he walked through the doors looking like he'd had the wind knocked out of him, she realised that he needed her more then ever and it definitely wouldn't be a good idea to tell him that she was expecting.

He sat down at the console and began to fiddle with his beloved ship. He didn't seem to notice the three of them looking at him in concern.

"Doctor?" Rose asked gently. She shook him a little bit. "What happened?"

The Doctor took a long deep breath and said: "He's dead. The Face of Boe, he died after talking to me."

"What did he say?" Rose asked, softly.

The Doctor swallowed, sighing as he ran his hands down his face. The humming of the TARDIS lowered, as if his ship knew what he had been told.

"Sorry," Rose hastily added, "Its private, I know."

"No, no, it's alright." He tried to smile but nothing came of it. "He said…he said that 'You Are Not Alone', meaning that in someway I'm not the last of the Time Lords. But it's impossible. I would know if they were still alive…And before you ask Rose, Time Lords cannot hide from each other."

"You don't think its true then?" Martha asked, confirming his own beliefs.

"No, it can't be. The Face of Boe was mistaken. Nothing could've survived the Time War." Not even that ship I sent out…that was destroyed in the blast. He sighed heavily. "They're not coming back. I'm alone."

"But you have us."

He smiled. "Yeah, I have you Martha Jones, Rose Tyler and Mickey Smith to keep me company, despite the fact that you can be blithering idiots sometimes."

Rose scoffed, hitting him on the arm. "Blithering idiots?"

"Well, sometimes, not all the time." He replied, but this time they could see the glint in his eyes that showed that he was pulling their legs.

"It means me."

Martha was taken back by the blunt comment. "What?"

"Think about it," Rose urged, shifting in her seat to face Martha. "The words 'You are not alone' mean me."

"Now I'm confused," Martha chuckled and turned her head to see Mickey chuckling. "What?"

"I think, what Rose means, is that the words are referring to her baby. Makes sense doesn't it?"

Martha nodded. "I suppose…but the Doctor told me about when you and he went to New Earth the first time. He said he was called there and he saw the Face of Boe there. I'm certain he said that there was something that he had to say to him but he refused to because he wasn't dying anymore. If that friend of the Doctor's knew something then, it can't refer to your child."

Biting her lip Rose sat back. "The Doctor would know if there were other Time Lords out there. He would be able to feel them in his head, like a link – like the one him and I share. But he can't. So the words must refer to me."

"If you say so," Martha accepted, "but I still think there is something more to this."

"You may be right," Mickey added, "It could be you Rose, but it might not. By all accounts it probably is...but I doubt this Face of Boe – or whatever his name is – would know of you getting pregnant in the future. They could be in hiding, but at the moment the most obvious choice is that it is something to do with you."

Martha continued: "Until we know the truth making assumptions will only make it harder to accept that we may be wrong."

"That doesn't look right?" The Doctor muttered as he peered into the computer screen as he fiddled with the TARDIS' controls. "That really shouldn't be there."

"What's that then, boss?" Mickey replied, grinning.

The Doctor scowled at him. "Don't. Just don't. I'm not your boss."

"I know."

He saw Martha and Rose walk into the console room. He clasped his hands together. "Right then, I have detected something that really shouldn't be on Earth."

"The TARDIS did, not you."

"Stop it Mickey." He warned once again, getting frustrated.

He saw Rose give her ex a sharp look who grinned back at her, but he did shut his mouth. "Good. Now then, I have discovered a source of energy in Cardiff. We are going to go and find it as it shouldn't be there."

"And what is it?" Martha asked, ever curious.

"Time-Energy. The last time I ever detected that was before the War ended." He fell silent, his face going from happy-maniac to sad. He spoke low. "Time Energy is in me. And the only way to produce Time Energy and to make it appear is to use a Time Lord. So it is a bit confusing."

"It could be to do with the words." Martha added. "Perhaps your people are still alive but you can't sense them because someone is preventing them from doing that."

"Now that is impossible." The Doctor answered. He saw Rose throw Martha a triumphant grin. What was going on between them? He wondered. He chose to ignore it and input co-ordinates before pulling the lever down and sending the TARDIS into the Vortex, heading right towards Cardiff in the year 2009.

He stepped out of the TARDIS that had settled itself outside an old factory that seemed to be falling apart. Inside his mind he could feel the energy pulling him towards it. He turned to look back at his three companions. "Stay here."

"No way," Rose demanded, "We're coming with you."

He couldn't really argue. Either way they would follow him. He smiled lightly as he stepped forward; ignoring the feeling in his mind that something was not just quite right.

"Are you okay?" Rose approached him, striding alongside him as he continued forward.

"Yeah, I'm fine," he replied, a little too hastily.

"Doctor! Why are you glowing?" Mickey called from behind.

Rose glanced down as the Doctor noticed that he seemed to be dosed in a light glow.

"I think I may be reacting to the Time Energy. It happens. Back on Gallifrey the glow never showed because the planet was so soaked in the energy. If this energy was located in the heart of a city rather in a disused factory then it would be a lot harder for me to get close."

"Thankfully it's not," Rose added.

As they reached the door, the Doctor reached into his pocket to retrieve the Sonic Screwdriver, however he was stopped by Martha laying a hand on his arm. "It's already open."

He hadn't noticed that. Taking tentative steps forward he pushed the door open and walked into the dark, abandoned factory. The others followed behind him.

"I'm glowing now." Rose mentioned holding up her hand and examining her fingertips. "Only faintly though…"

"That shouldn't be happening." The Doctor muttered.

"Why not?" Rose asked.

"You're human, not a Time Lord. Only Time Lords should be affected by this."

"Ah," Rose placed her hands in front of her stomach, a sense of worry building within her.

"Rose, is there something you are not telling me?" He asked, fear evident in his voice.

She bit her lip and shook her head. "No. There isn't."

He saw Martha and Mickey exchange looks and he felt concerned about Rose's welfare. She was keeping something from him, that was certain, but she had chosen not to divulge it yet. He took a deep breath. "Okay. Let me know if there is something you are not telling me because there is no way you should be soaked in that energy. It could do you harm and I can't lose you again."

"I know." Rose responded, keeping her eyes level with his. "And I will tell you if there is something I need to say."

"Good." He turned away, but deep down he had a feeling what she wasn't telling him. He could pry into her mind through their mind link however that would be rude to do so without an invitation. All he could do was wait until Rose told him the truth about her condition. "Come on, slowly now."

He led them through the factory. The glow surrounded him substituted enough light for them to see what was around them. Machinery was rusting away and little beads of light shone down on them from the ceiling where the roof was slowly crumbling to pieces. Then he heard voices. He held his hand up, stopping the others.

"Someone else is here." He whispered.

Very slowly he inched forwards. The glow around him brightened considerably as they rounded a big stack of boxes that substituted as a wall. His eyes widened as he saw the one person he hadn't expected to see; someone who bent the law of physics. This man should, by rights, be dead but he was alive, standing right before them.

"Doctor? Rose?"

He hesitated wondering how he could deal with this problem. Jack Harkness was wrong. The Doctor's intuition was to run away, but he had more pressing problems, especially since, like himself, Jack was glowing to. And then it hit him. The answer was so simple.

The Time Vortex!

Rose had held it within her long enough for her power to form, but Jack was a direct result of Rose's actions. He was a product of her power and like her, now was a constant part of the Vortex. In some ways, Rose was wrong to, but he wasn't afraid or scared of her like he was with Jack.

Rose ran forward, wrapping her arms round Jack, lifting her up. He kissed her on the cheek.

"Rose! It's good to see you! I thought…" he struggled to find words. "I thought you were dead."

"Dead?" Rose repeated, "Where did you get that idea from?"

"You were listed among the dead after the battle of Canary Wharf."

"Oh," Rose wished she hadn't forgotten what the Doctor had said. Of course Jack would know, but then how did he get back to earth when he had been left behind in the future last time she had seen him? "How did you get back?"

"I used my Vortex Manipulator." Jack answered. He showed her a device wrapped round his wrist. "It allows me to travel in time." He glanced over at the Doctor, who stood watching, the glow around him brighter then ever.

"Doctor?" Jack said, unsure if it was him.

"Captain."

Yes, it definitely was him. Though he did wonder how he had changed…

"Like the new face." Jack winked, hoping to stir a laugh from him.

The Doctor just continued staring. A flicker of fear could be seen in his eyes.

Rose looked back and forth. "What's going on?"

"Yes, we would like to know what is going on too!"

Jack glanced over his shoulder to see Owen glowering at him.

"Who the hell are they? And how do they know you?"

This was going to be one long explanation.

To be continued…

Please let me know what you think!

Thank you for all the reviews and support you've given me so far! Until next time – Tenth-Doctor-Fan