Disclaimer: Doctor Who belongs to the BBC. I do not own any of it, nor do I make any money from it.

A/N Thanks for the response on the last chapter. I am sorry that I haven't been updating but the site wasn't sending out alerts for some reason. And then, my laptop broke down meaning I lost about a week's worth of writing. Thankfully, I have a new laptop now and I have finally caught up to the point where I was a week ago.

Anyway, here is Part 3 and a twist at the end.

Happy Reading!

The Clone Wars: The Segment

Previously

"To the left!" Commander Styx commanded and the Sontarans, and Amy and Rory began their trek through the narrow passageways under the surface of the asteroid to get to the segment.

Meanwhile, the Doctor and Rose had followed the Rutans on a path through a cave in the cliffs and into the catacombs. They were moving right steadily, towards the segment. The Doctor was holding Rose's hand as they walked, both of them being mindful of the fact that any corner they turned at could have the Sontarans waiting to ambush them.

In the deepest of the caves where the Heleonic segment was resting, its guardians cackled in amusement as they watched the Sontarans and Rutans try and enter their domain through opposite ends.

"Soon," said their leader as the rest of them laughed loudly. "They shall be here soon. And we shall be avenged at last."

The Doctor and Rose had been walking for about half an hour with the Rutans when a worried expression crossed the Doctor's face. Rose looked at him questioningly and he leaned closer to her to answer.

"The core is giving a signal," he whispered. "Straight ahead."

"The way we are going?" she asked. "That's good, isn't it? If the Rutans and Sontarans are fighting, we can get the segment easily."

The Doctor pursed his lips and pulled her to a stop while the Rutans got rid of a blockage in their path. "I need your shirt," he said.

Rose looked at the bright pink tank top she was wearing under her darker pink hoodie. She raised her eyebrows at the Doctor. "I don't know if it's your colour," she joked lightly.

The Doctor looked a bit perplexed. "Nonsense," he declared. "I know for a fact that I can carry off pink quite well. But that's not why I need it."

"Why do you need it then?" asked Rose.

"To leave a message for Amy and Rory," he said. He held his hand out impatiently.

Realising that he was not joking, Rose shrugged. "Do you need it in one piece?" she asked in a matter of fact tone. She'd had far weirder requests from him after all.

"It's not a requirement," he said dryly.

Rose nodded and zipped up her hoodie. She reached under it and with one single tug, had her tank top torn from her shoulders. The Doctor watched with an impressed look as she handed him the remains of her pink tank top without ever taking her hoodie off.

"Thank you," he said and then reached into the pocket of his coat to pull out a thin, metal rod about three feet in length. "Keep a look out," said the Doctor.

Rose chanced a quick look towards the Rutans and saw them attaching minor explosives to the blockage in their way. None of them were paying close attention to the Doctor or her. She looked back at the Doctor and saw him mounting her pink shirt on the rod like a flag. Before she could ask what he was doing, he wrapped an arm around her waist and pulled her tightly against his body. She didn't have a chance to ask before a loud explosion rang behind them.

"Are you okay?" she heard him ask her and she nodded hastily, trying not to shiver because of his cool chest against her body. "Some warning would have been nice!" he snapped at the Rutans who ignored him and began to move forward.

"What is that flag for?" Rose asked as the Doctor hid it inside his coat and pulled her after the Rutans.

"Can't you feel it?" he asked her. At the blank look that Rose gave him, he looked genuinely annoyed. "Sometimes I envy human minds," he muttered.

"Oi!" snapped Rose, punching his arm, being mindful not to hit an injured spot. "Enough of the condescending attitude."

He rubbed his arm with an exaggerated scowl. "There are strong telepathic waves through here. And for some odd reason, they are very familiar to me."

"Sontarans aren't telepathic, I'm guessing," said Rose.

"No, they are not," said the Doctor. "I have a feeling there is more at work here than we have been led to believe."

"SONTAR-HA! SONTAR-HA! SONTAR-HA!"

"Don't they ever stop?" grumbled Rory.

"No," said Amy, looking just as tired of the chant.

"Do we have a plan?" he asked her in a low voice.

"Well, no," said Amy.

"Great," said Rory, sarcasm evident in his voice. "So, we are just walking into a big ambush with no plan. Brilliant."

Amy laughed and patted his cheek. "We're just going to wing it," she said with a bright grin.

"Wing it?" Rory smiled despite himself. "Where'd you hear that one?"

"One of your 21st century films," said Amy. "It was in the right context, wasn't it?"

"Yeah," agreed Rory with a laugh. "Yeah, it was."

"HALT!" ordered Styx and Amy and Rory came to a stop with the rest of the Sontarans. "We shall regroup in order to discuss tactics. The human scum will stay here."

Amy and Rory glared at Styx as the Sontarans huddled around each other. "I am really tired of being called 'scum' by potatoheads," muttered Amy as she and Rory stood to the side. She looked at Rory who was rubbing his head. "You alright?"

"Yeah," he nodded. "Getting a bit of a headache."

Amy ran a hand through his hair almost absently and he stared at her in shock, a blush rising on his cheeks. "Sorry, did I do something wrong?" she asked, slightly thrown by the look in his eyes.

"No, no," he said at once, ducking his gaze. "Amy, I was wondering if…"

"Keep moving, human scum!" Styx ordered and whatever Rory was about to say was cut short. Amy could have smacked the potato for that. Especially since it had looked like Rory was finally going to make a move on her.

As they started their trek back up again, Amy wondered what exactly Rory would have said. Would he finally have asked her to start a romantic relationship with him? As a woman of the 52nd century, Amy had no problem with going through lovers like clothes but Rory was different. Even from the time that he came in, he had known Amy long enough to make a move but he hadn't dared for reasons Amy hadn't understood. Finally, this morning when Rose had helped her pick out the old Earth clothes, she had mustered up the courage to ask Rose for some friendly advice.

"Rory is different," said Rose as she tossed her the skirt and leggings. "He's shy and he respects you far too much to go in for a one-night stand."

"How do I get him to make a move then?" asked Amy as she pulled her new clothes on.

"Ease him into it," said Rose. "Flirt with him a bit more. Let him know you are interested."

"I thought I was already doing that," snapped Amy indignantly.

Rose had giggled. "Amy, you flirt with everyone we meet," she pointed out.

"So, I should pay more attention to Rory?" she asked, as if that was a bit of an odd concept.

Rose nodded. "Yeah, you do that. And if he doesn't ask you after that, I'll be sure to smack some sense into him."

Said man in question was still rubbing his head and Amy squeezed his hand comfortingly. "Don't worry, we'll get out of it," she promised him.

He smiled gratefully at her as they reached a wide chamber lit by solar lamps. "This is it," he whispered. "Any sign of the others?"

Amy ran her eyes around the chamber but couldn't see anyone around. Yet the hairs on her arms were raised like she was being watched. She moved closer to Rory. "Get ready to run," she whispered to him.

"Where are we going to run?" he hissed back.

Amy had to concede his point when she saw something pink out of the corner of her eye. She nudged Rory and pointed towards it. "The Rutans are here. Once they come out and start fighting, run to the pink flag," she whispered.

"SHOW YOURSELVES, RUTAN SCUM!" Styx shouted as the Sontarans picked up their chant of 'SONTAR-HA!"

"Now!" Amy yelled as the Rutans descended from their hiding places around the chamber. Amy and Rory ran towards the pink flag and were surprised to find a narrow passageway just out of sight. They entered it and found the Doctor and Rose crouching inside, who put a finger to their lips, asking them to be quiet.

In the chamber, it was chaos as the Sontarans and the Rutans battled it out. The Sontarans had good weapons but the Rutans could change their shape and create shields and better defensive tactics. Neither race was particularly interested in the human hostages that they had taken, nor were they concerned about the Heleonic segment for which this whole thing had been about.

"DIE DIE DIE DIE," Styx was yelling as he fired bolt after bolt.

The numbers were falling in equal measures on both sides and each side had summoned more forces from their respective ships. From their hiding place, the Doctor drew out the core to the Key to Time and pointed it towards the chamber.

It was pointing to a large red crystal encased in a transparent cube, hanging from the ceiling. "How are we going to get that?" murmured Amy.

Below the segment, the Sontarans and Rutans were fighting violently. "Hang on," said Rory. "I just want to try something."

Before anyone could stop him, he emerged out of their hiding place and picked up the makeshift pink flag that the Doctor had used to draw their attention. The Sontarans and Rutans paid him no mind as he kept his back to the chamber's walls and walked around the fighting. The segment was still glowing lazily as Rory tore off the shirt from the end of the 'flag' and used the metal rod to loop around the wiring holding the segment up.

Being mindful of the fighting factions, he tilted it towards himself and with a final tug, the crystal flew through the air, landing in his hands. He looked around quickly but the two clone races were completely unaware of his theft. He started to move back towards the hiding place where the Doctor, Rose and Amy were. He was almost there when Styx gave a roar.

"THE SEGMENT!" he screamed and even the Rutans stopped fighting. "The human scum have taken the segment."

Rory broke into a run after the Doctor, Rose and Amy through the narrow passageway. The Doctor was in the lead and he seemed to have some idea of where they were going. They heard sounds of pursuit behind them but it appeared that some of the Sontarans had got stuck in the narrow passageway and the Rutans who could have fitted more easily were busy fighting those caught Sontarans.

As they ran, they heard a loud explosion behind them and Rory ran into Amy's back with a painful wince. "Why'd you stop?" Amy asked the Doctor.

"Ssh," ordered the Doctor sharply. "Listen."

The four of them were quiet for a moment before Rose broke the silence. "Listen to what?" she asked.

"Exactly," said the Doctor. "It's gone quiet."

"So?" asked Rory. "We heard an explosion. Maybe one of the clone races decided to detonate a bomb."

The Doctor looked past Amy and Rose, and nodded at Rory. "Yes, that seems likely," he said. He tilted his head at Rory and walked towards him slowly. "Give me the segment, Rory."

Rory's grip tightened on the segment. "I can hold onto it," he said.

"I would prefer if I had it," said the Doctor in the same cautious tone.

"Doc, chill out," said Amy. "Rory will look after it."

The Doctor ignored her. "Rory," he prompted.

"No," said Rory, holding the segment away from the Doctor. "I mustn't give this to you."

"Rory, what're you on about?" Rose asked, confused.

"I have to keep this safe," said Rory, holding the crystal close as if it were a precious child.

"What's wrong with him, Doc?" Amy asked, looking scared.

"Rory, listen to me," said the Doctor, in a serious voice. "We are coming for you, Rory. We will find you. Tell the Vardans that. The Doctor is coming."

"Doc, what is going on?" Amy demanded, almost hysterical at this point.

"I am so sorry, Rory," said the Doctor and pointed the sonic screwdriver at Rory's head.

Rory screamed loudly in pain as he started to flicker in and out of existence. His body vanished completely, leaving a silhouette of a papery silver frame. It fluttered angrily at them before dissipating completely.

Over on the Vardan ship, Rory's eyes snapped open and he realised just how many scanners he was attached to. He looked up and saw several of the silver papery figures rustling and muttering amongst themselves.

He had to strain his ears to hear some of the words but he finally understood the gist of what they were saying.

"The Doctor has killed one of the Vardans we sent in as an impostor for the human male."

"He has threatened to attack."

"Prepare our defences."

"Put the human male in stasis."

"The Doctor must not be allowed to defeat the Vardans again."

"This time we shall be avenged."

A/N End of Part 3. Thanks for reading.

So, what did you think? I did say that they were known aliens attached to the Sontarans. For those of you confused, the Vardans were seen in 'The Invasion of Time'. The next chapter will explain exactly how Rory and the Vardans were linked. Be mindful that this is nothing like "The Flesh" we saw in Series 6.

Anyway, let me know what you thought of this one. The final part will see the Doctor, Rose and Amy launching a rescue for Rory. Let's see how that goes. It will be up soon.

~ Phoenix