Still don't own Doctor Who, or its characters. I also don't own Fullmetal Alchemist or its characters. I really like the idea of physical representations of the seven deadly sins. Hope you like my use of them!

As always, read and review!

Chapter 3
Martha and the Doctor Reunited

Sean woke up with his head ringing. From the light outside, night had clearly passed into day.
"Shit," he swore. "I must be late for work now." He stood up and had to grab the wall for balance as the blood rushed out of his head. "Whoa," he said. "Maybe I should take it easy for a bit after last night." It was that moment when he realized where he was.
He looked around and it hit him that he was not in his bedroom. He was in a rubble-filled room and there was a big hole in the ceiling. The memories from the previous night came flooding back to him. "Damn," he said to himself as he remembered Miss Jones...Martha...standing naked in front of her window. "I wonder where she went." He looked up at the hole above him, gauging how high it was, and if he could actually climb out of it in his current state. He shook his head a couple of times and judged that he was fit enough to at least try.
Then he remembered the box. He turned around and there it was on the floor behind him, tipped over on its back with the lid open.
He approached it warily and looked inside. It was empty. It was then that he noticed it was no longer glowing. It wasn't even orange or violet or blue. It was the plainest piece of wood craftsmanship he had ever seen. It was just an ordinary box.
"Huh," he grunted. He bent down to pick it up. It weighed as much as an ordinary box now too. Whatever had been inside before must have been extremely heavy or dense. He looked back at the hole. Yes, he thought, he could manage to climb the pile of rubble while holding the box.
He walked over and carefully started up. He had to go slowly in case there were unstable pieces of concrete. As he neared the top, there was a small scare when the rock he was standing on gave way and he had to grab quickly onto the floor above him. He just managed to hang on long enough to gain another foothold. He put the box up on the floor above him and pulled himself using both arms. His legs scrabbled at the debris below, which gave way just as he rolled onto the dusty carpet above.
"Well, that went well," he said to himself. He reached down and picked up the box.
Part of him wanted to think that it had all been a dream, but he knew it wasn't so. The evidence for the reality lay in the fact that he had woken up exactly where he had blacked out when he opened the box. He closed and latched it now. It still made him uneasy, even though he did not know what exactly had come out of it but a huge blast of energy.
As he looked at the floor, he noticed that there were bare footprints in the dust, and then the dusty trail leading out of the house. They couldn't have been Martha's, she had been wearing boots when he had seen her last night. So someone else had been down there with him and left before he had woken up. He followed them for a bit, but lost them when they reached the grass.
Sean had never been much of a hunter, even when he had gone with his father every fall. His father had tried to teach him how to track and trap game, but he could never get it right. Bent blades of grass just evaded his gaze whenever he had tried, and he was useless at lashing together a trap.
He sighed and stood up. He looked over at Martha's house. "Maybe I'll just go ask her what is going on," he thought.
He walked towards her house, still clutching the box. As he drew nearer, he could hear the sounds of heavy things being thrown about and crashing into the walls inside. He held the box up, as if to use it as a weapon, and ran towards the door. It was unlocked. He threw it open and looked around. Everything was in disarray. Tables and chairs were overturned, and a light fixture was on the ground, the glass broken into what seemed like a hundred shards. He moved quickly to where he heard the noises coming from.
"Martha!" he called out as he ran through the kitchen and into what appeared to be a living room. Inside the room were eight figures. Seven of them were surrounding one that was prone on the floor. It was Martha Jones.
"Martha!" he cried. The seven figures whirled at the sound. Well, most of them whirled. There was a particularly fat one that moved slowly, and one that just moved slowly, as though the effort to move took a great effort, although it looked strong enough. The smallest figure hissed at him.
They were humanoid, although they were covered in strange markings, and oddly dressed. One marking in particular was common on all of them, although it showed up in different places on their bodies. It looked like a snake biting its own tail.
One figure, a woman, stepped away from the others towards him.
"You would be wise to leave this place," she said. Her eyes were an intense shade of violet, the same color that the hinges had been. She glanced down. "But leave that behind with us," she said, gesturing at the box.
"What do you want with this?" he asked, sounding braver than he felt. He glanced at Martha, and was horrified to see that she wasn't breathing. He swallowed hard. "It's just a silly old box."
"That silly old box," she said with a cold smile, "is our ticket out of here and onto Olympus."
Sean raised an eyebrow. "Olympus?" he said. "Do you mean Mount Olympus, home of the gods?"
Her eyes narrowed, and the smile disappeared, revealing a snarl. "What could you know of the gods?" she asked icily. "You are just a mortal."
He snorted. "I know that the gods aren't real," he said. "They're myths. Made-up legends to explain away the seasons."
There was a cry from behind the woman. The fat one was sucking on his finger. "What does the human mean?" he asked.
"He lies," said another voice. This one came from the figure with the long, spiky hair. "He knows nothing of them, only what he has heard told to him." The voice, and the person it belonged to, was androgynous. Sean couldn't tell if it was a man or a woman. But it was full of hate; that much he could tell. "They're fairy tales to him," the person continued. "But they're real, all right. More real than the pathetic God this human does believe in."
Sean's blood boiled at this. He had been brought up in a Christian family, and had questioned his faith in the past, but he knew what he believed. How dare this creature belittle his faith!
"They never existed!" Sean shouted. He knew he had to get these things out of there somehow, and get Martha some kind of help, even if it was too late to save her life. Who knows what they would do to her if he left them alone.
"The Greeks, the Romans, the Egyptians, the Norse…they needed something to believe in; they needed some explanation for all of the things that were happening in their lives. We now understand these things through the explanations of science."
"Just because something can be explained through science," said the smallest figure, a little boy, "doesn't mean it wasn't caused by a higher power." He smirked. "Don't you believe the same thing about your God? This is not so far from that."
Sean was about to retort when he heard a strange sound. It sounded like a strained breathing, but coming from a machine. His surroundings began to change, and the creatures were fading out of view. Fading into view was a big console and a very large room and what appeared to be steampunky, coral decorations. A funny looking man with long hair and a bow tie was running around the console. When everything had become completely solid around us, the man ran towards the prone figure of Martha.
"Martha?" he said quietly, leaning over and touching her face. "Don't you do this to me now, please," he implored. He was British too, judging by his accent.
She didn't move. The man pressed his ear close to her chin, listening for breath, and looking for a heartbeat on her chest. From the look on his face, he wasn't getting anything.
He looked up at Sean, and there was fire in his eyes. "This is one of my friends," he said, and the anguish in his voice was palpable. "I swear, if you had anything to do with this, I will end you, and there will be no trace of your having ever existed."
Sean could tell that the man meant it. "I didn't do anything to her," he said. "I promise. It was those...those things, out there."

The man ran to the console and pulled up a viewscreen that looked like a computer monitor. Outside they could see the things gathering around the room we were in. Sean didn't understand how they were in such a large space when the room that they were inside of was so small. Surely the house around us would have been destroyed by the sheer size of the space we are in, thought Sean to himself.
"Oh no," said the man. "It's the Homunculi."
Sean frowned. "What are homunculi?" he said.
"They're mistakes," said the man. "They occur when someone wants to make himself pure and incapable of sin, according to the Christian bible." He paused and glared at the creatures. "Someone attempted and succeeded in removing the pieces of himself that were capable of the deadly sins. Lust, Envy, Sloth, Greed, Wrath, Pride, and Gluttony. But no human can truly exist without the capability to be evil. It's like a removal of free will. That's why we have to find out whoever created these monstrosities and send these things back inside him."
"So these things," said Sean, "are pieces of a person's soul, essentially?"
The man nodded. "And yes, a side effect of removing these things does, in fact, make one immortal. Just like Voldemort." He looked at Sean. "The reason is that when man first committed sin, the privilege of living forever was taken away from him. God said that if you eat from the tree, you would surely die. Now, He didn't say exactly when you would die, but they assumed it was an automatic thing, until the serpent twisted the words around."
"Are you a Christian?" asked Sean.
"I believe in Jesus Christ, yes," said the man. "Nice fellow. It's a shame, what happened to him. But it was a fixed point in time, so I couldn't do anything about it. I wouldn't have anyway, because I knew he'd be back a few days later."
Sean blinked. Something clicked in him. "Fixed point in time," he said. He had heard Martha say those same words the night before. "Are you the doctor that Martha was talking to last night?"
"Not sure what you're talking about," said the man. "I haven't heard from her in centuries. I'm the Doctor, nice to meet you. Hold on." The Doctor stopped and looked closely at Sean. "Who are you?"
"I'm Sean," said Sean. "I live just across the street from here." He pointed in the direction of his house. "Martha had just moved in."

The Doctor frowned. "I keep track of all of my companions. I knew something was wrong just a few hours ago. As far as I am concerned, Sean," he said, angrily emphasizing the name, "Martha Jones isn't supposed to be here at all!"
Sean held his hands up in a gesture of surrender. "All right," he said cautiously. "I'm only telling you what I know." He looked around. "And what I don't know and am very confused about is, what the f*** is this thing?

"The Doctor pointed a finger imperiously in Sean's face, centimeters from his nose. "First of all, there's no need for the language. This is a children's show, after all. That should be bleeped out. Censors!" he called out.
The censors noticed and went back to the script and bleeped out the foul word.
"Thank you!" said the Doctor. He smiled at Sean. "I've got timey-wimey powers," he said, "so I'm allowed to do things like break the fourth wall. As for this thing," and he gestured his arms broadly around him, "this is my TARDIS. It stands for Time And Relative Dimension In Space."
"Oh, so that's why it's bigger on the inside?" said Sean skeptically.
"Yup, that's right." The Doctor clapped his hands together. "The outside looks just like your standard police box from the 1950s in England, and it's stuck that way." He winked. "And I wouldn't have it any other way. It's made to blend in to any environment through the chameleon circuit, but that malfunctioned ages ago when I was here with my granddaughter."
The information was overwhelming to Sean. "Okay, Doctor, what are you saying?" Then it hit him. "You're from a special organization in the government, aren't you? Where are the Thompsons?"
The Doctor sighed and threw his hands up in exasperation. "I suppose that's the cool thing, is it? Having a time machine developed for the government?" He stuck his finger back in Sean's face. "I know what cool is, and the government is. Not. Cool!" He paused, his breathing a bit ragged. "Now bow ties," he said, adjusting his own, "bow ties are cool."
"So you're not from the government?" asked Sean.
"No, I'm not," said the Doctor smugly. "Though I did work for U.N.I.T. at one time. More on that later. Care to guess again?"
Sean had no clue what U.N.I.T. was, but he thought for a moment, and he could only think of three other possibilities for the existence of a time machine.
"You're either a private inventor, you're from the future, or you're an alien." He said these last words with as much skepticism as he could muster, though admittedly his doubts about the fantastical had been worn down due to the fantastical things he had already seen.
The Doctor smiled proudly. "Two out of three's not bad," he said. "I didn't invent this," he said, beckoning to the TARDIS' console. "But my race did. I just borrowed it and escaped."
"Escaped from what?" Sean asked, very interested now.
The Doctor hesitated. "I'm a Time Lord, and there was a Time War with a race called the Daleks. I borrowed the TARDIS...well, I say I borrowed, I really stole it, or rather she stole me, long before the war. When it came about, I...can finish that story later. It's not a pleasant subject. Besides!" he exclaimed, clapping his hands together. "We have more pressing matters to attend to!" He turned back to Martha. Sean followed him.
"What about the homunculi?" he asked.
"Oh, don't worry about them," said the Doctor. "They can't get in any more than the assembled hordes of Genghis Khan could, and believe me, they've tried." He stopped suddenly and shuddered.
"What's the matter?" asked Sean, concerned.
"Deja vu," said the Doctor, "which, for a time traveler, is a lot more important than the feeling of someone walking over your grave, and more literal than that as well." His eyes grew distant. "I've spoken those words before, or very nearly." Then he brightened. "That gives me an idea!"
He jumped back to the console. "But Doctor," said Sean, "what about Martha?"
"Oh, she's fine, don't worry," said the Doctor. "Or she will be." He started messing around with the controls and the TARDIS made the heavy breathing noise and the machinery started to move. "Mind you," he said, "the idea I have is quite mad, and probably won't work, and could in fact create a massive paradox that will destroy two-thirds of the universe."
"What's that?" asked Sean, holding on to a railing as the TARDIS rocked about like the bridge on the Enterprise when it was under fire.
"Crossing my own time stream!" shouted the Doctor, laughing. "I haven't done that in centuries! I just have to make sure I don't accidentally run into myself." he said seriously. "And if I do, I definitely can't touch myself. The consequences could be dire."
Sean almost laughed, but the Doctor now looked very serious, and very dangerous. He nodded. "Let's do it," he said.
The Doctor grinned. "Here we go!" And they landed.
"Where are we?" asked Sean.
"In orbit above the Earth," said the Doctor. "We're on Satellite Five, and a friend of mine is about to do the stupidest thing any of my friends has ever done, and I couldn't ever thank her enough for it, especially now."
"Why?" asked Sean. "What did she do?"
The Doctor smiled the happiest smile Sean had ever seen. "She's about to save Martha Jones' life." He bent down and picked Martha up. She lay limply in his arms. "Get the door for us now, Sean."
Sean turned down around and saw a normal wooden door. He went to it and opened it.
"EXTERMINATE!" a metallic voice cried. What looked like a large trash can which tapered out to the bottom and a whisk and a plunger sticking out like arms was right in front of the door. All of a sudden, a blue light shot out of a hole in the end of the whisk right towards Sean. Fortunately, the Doctor had thought ahead and turned on the force field around the TARDIS.
In the next moment, the trash can disintegrated in front of their eyes.
The Doctor was now grinning from ear to ear. "She's done it," he said. "Any moment now…" and he looked expectantly down at Martha in his arms.
Sean stared at Martha as well, not knowing what he was waiting for. The Doctor had said she was fine, but the fact that she wasn't breathing when he first came upon her, and she still wasn't breathing now, really didn't convince him that she was, or would be, fine.
"Um, Doctor?" he said, "I'm not a doctor, but I think she's gone."
"Shut up!" said the Doctor. "She's going to be okay! Come on Martha Jones, don't you dare give up on me!"
Her eyes opened suddenly and she gasped a huge breath, as if she had been holding it in for a long time. She smiled weakly at the Doctor. "Never," she said.
The joy on the Doctor's face was palpable. "Oh, Martha," he said, kissing her forehead. "Don't you ever do that to me again." His eyes widened as though he just realized something terrifying. "And now you never will."
Martha shook her head. "Don't be stupid, you daft man," she said, laughing as he set her down in a chair. "Jack told me about what happened to him a long time ago, and I knew that if I was dead, you would do whatever you could to bring me back, regardless of the consequences." She stood up shakily and crossed her arms. "So I decided to play a little joke on you."
The Doctor furrowed his brow. "You mean," he started to say.
"That I've been okay all this time?" she finished. "Yeah." She smiled. "I can hold my breath for a really long time, you know."
The Doctor looked very angry now. "I have lost too much to be played with, Martha Jones!" He looked like he were about to shake her.
She took a step back. "I'm sorry, Doctor," she said, clearly terrified. "I didn't mean to-"
"Didn't mean to what?" said the Doctor. "Make my hearts stop altogether?" He looked at Sean at this. "Time Lords have two hearts. It's very handy in case one stops, but honestly, how do you humans handle running on just one?"
He looked back at Martha, and the fire was back. She sat down, hard. "I'm sorry, Doctor."
His gaze softened. "I know, Martha. But you have to understand. I'm the same person I was when I first met you, or very nearly. Do you know what I had to do to Donna?" She nodded. "What about the Ponds?"
"Who are the Ponds?" asked Sean.
"My best friends," said the Doctor, and his voice broke. "And I couldn't do anything to save them." He looked at Martha. "It was the angels, Martha."
She gasped, her hand going to her mouth. "You couldn't go back to get them?"
He shook his head. "Their time was locked away from me forever. But at least they were together." He sighed and leaned against a nearby railing.
Martha stood up warily and walked over to him. She wrapped her arms around him, and he returned the hug as if she would slip away if he let go.
"I'm sorry, Doctor," she whispered.
Sean still wasn't sure what they were talking about, but he felt as though he were intruding on a private moment. He felt very uncomfortable.
When the two of them finally let go, Martha smiled. "And a new face now I see! What's with the bow tie? Haven't seen you in one of those since Doctor Lazarus."
"Bow ties are cool, Martha Jones," he said quietly, straightening it.
She smiled. "You look younger, but your eyes are so much older now. You've seen more things than I can imagine, haven't you?" He nodded.
"And so much that I want to forget," he muttered. He looked up at Sean and clapped his hands together. "Now we need to figure out what's going to happen with you and those homunculi."
Sean stood up, not realizing that he had sat down. "Well, we have to know what they're going to do and where they're going to go, don't we?" He hesitated. "I let them out, so I'm responsible for putting them back where they came from." He wasn't sure that they had come from the box until that moment, but now he realized they couldn't have come from anywhere else.
The Doctor nodded. "So, a good place to start would be the Jones residence, just to see if they're still there." He grinned at Martha. "Geronimo!"
Her shoulders sagged. "What happened to 'allons'y'? I liked that word!" she said, almost whining.
"Come along, Jones!" he said, and ran back into the TARDIS, Martha at his heels. The door had almost shut when Sean slipped inside.
As it shut, Sean could swear he heard an American voice shouting the Doctor's name, and running footsteps. But he put it out of his mind. No time to worry about it now.
The Doctor was busy at the console, turning various switches and knobs. He pulled a lever, and the TARDIS started moving again, leaving Satellite Five behind.