A/N: I am not planning on this being a long story. At the moment this is just going to be a side story I work on while I try to get over my writer's block for the main story I am currently working on. This is an idea that has been in my head for a little while. I am not sure how many chapters this will end up being. A typical story for me has chapter lengths at around 20 pages. The chapters for this one will not be that long. Maybe in the future this will get longer, but I am not making any promises. Since the chapters will be shorter than what I am used to writing, that should mean that updates will be somewhat regular.

Disclaimer: I will only say this once. I do not own Doctor Who or Smallville.

Area 51

Chapter 1: The arrival

"Doctor where are we going this time?" Clara asked the tweed covered alien.

"Somewhere I had hoped I would never have to go, but the future is changing. Events that were never supposed to happen have happened. I need to fix this or the whole future will change and not for the better,"

"So where exactly is it that we are going that is so important to the future?" Clara asked, wanting to get a straight answer.

"We are going to Area 51, which I am sure you have heard rumors of, but most people think isn't real," said the Doctor. "We are going to get into Area 51 and break an alien out of imprisonment there. That shouldn't be too difficult."

"Have you forgotten that you are an alien?"

"Then it is lucky that our two species look alike. I will also have the psychic paper to get us in."

"Just don't get us locked up."

"I'll try my best. Hang on while we come in for a landing."

The TARDIS materialized as close to their destination as possible without being detected. At least no one saw them land. This was one of the few places where the Doctor wanted to be as discrete as possible. He proceeded to turn the TARDIS invisible before he and Clara left the safety of the time and space ship.

As they approached the front gate of the military looking base, Clara began to feel nervous and started to fidget a little with her outfit. The Doctor insisted she dress in a business suit while he remained wearing his long purple tweed coat. Clara thought they would lock him up just for his sense of fashion alone. What human would wear an outfit like that? All too soon they were at the gate and being approached by a guard.

"State your names and your purpose for visiting," commanded the guard.

"Well I am Doctor Smith and this is my assistant Clara Oswin," began the Doctor who did notice the slight look Clara had given him at messing around with her name. The Doctor pulled out the psychic paper and held it out before the guard. "We are here on strict and confidential business pertaining to someone being held inside this facility."

"You are going to need to give me a specific name or you are not getting a foot closer to this building," said the guard.

"We are here to evaluate the alien Kal-el," said the Doctor. "Is that specific enough for you?"

"You are here because of Kal-el?" The guard asked sceptically. "Why would they need to call you two in when we have a whole team dedicated to that thing?"

The Doctor tried to hide his grimace at anyone being called a thing. "Kal-el is a special case and we are the experts."

"Let me see your credentials again," said the guard. He took a long hard look at the paper and noticed something strange going on with the paper. He had suspected the first time he saw it that it was psychic paper, but now he was sure. He saw what he was supposed to see, but he could also see the flaws. This was required training for the guards so that they could not be tricked. They were also taught how to deal with those trying to trick them. "Everything here checks out. I'll lead you two to the front door and then I will just need you to step through the metal detector before going inside."

"Ladies first," The Doctor gestured to Clara. At the door Clara walked through the metal detector first without incident.

The guard was surprised when the scanner showed Clara Oswin to be human. Maybe he had been wrong. That thought only lasted for a second until Doctor Smith entered the scanner. An alarm went off and the scanner was sealed off, blocking the alien's exit. A scan of Doctor Smith showed up on a screen and showed two hearts. Besides the two hearts, the alien looked very human.

Clara was left standing on the other side of the scanner and was looking in at the Doctor. She didn't know what to do, but it was up to her now to get the Doctor free.

"Hey what do you think you are doing trapping Doctor Smith like that?" Clara demanded before more guards showed up and restrained her. Clara tried to get free, but there were too many. "We are here on official business. What is the meaning of this?"

"He must have her brainwashed well to have her behave like this," said a scientist who had just arrived. "Bring the girl to a waiting room and restrain her for her own safety. I will be with her in awhile to find out the extent of the brainwashing. Bring this thing to a cell. We don't know what abilities he has so we will just go for one of our stronger cells. Make sure to check him for any technology and I will be with him after I visit that girl he abducted to help get him in here. "

"Yes, ma'am," said all the guards in unison. The guards who were restraining Clara brought her to a waiting/ interrogation room while the others sent a knock out gas into the chamber the Doctor was currently in. Once he was unconscious they knew they had to work quickly since they didn't know how long he would be out for. They searched his pockets and pulled out a vast number of objects including a strange wand like device followed by a yo yo. Various other items were taken out until the Doctor's pockets were empty. He was then dragged to one of the strongest cells that just happened to be located near Kal-el. The wings were separated by the strength and danger level of the alien. One guard joked that this should now be the humanoid alien wing since the only two occupants were Kal-el and the new arrival.

Back in the interrogation room, Clara was not waiting around patiently and was yelling out for them to let her go. She shut up when a woman who was probably in her early fifties with glasses and her dark hair in a tight bun walked into the room wearing a lab coat over a plain dark shirt and pants gave her a stern look with just a hint of pity.

"I am Doctor Gustav and I am the head of the scientific division here. You are not the first one we have seen that has been influenced by a being from another world. In some cases we can get the person back to their right mind. We can get you therapy and we can make you comfortable. All we ask is that you tell us what you know about the thing that dragged you in here."

"He is not a thing," said Clara vehemently. "He is my friend and he has taken me on amazing adventures."

"That thing has taken you to space?" Doctor Gustav asked while making notes on her clipboard.

"I have seen the Universe and met so many different aliens some who are good and some who are bad just like here. There are good people and bad people. I can't believe how you have treated the Doctor. He is good and has saved his planet along with others multiple times."

"So you are trying to tell me that an alien has saved this planet many times? The brainwashing has gone much further than I originally thought. No alien would want to save our world. They either have no interest in us or they wish to conquer us. We are here to save the world from them."

"That's not true," said Clara shaking her head. "I have not been brainwashed."

"How did you meet this alien?" Doctor Gustav persisted with her questions.

"I had trouble with the internet and called a help line. Some weird guy answered who seemed unsure as to why I was calling him. He did help me with the internet and next thing I know he is showing up at my house dressed as a monk. I still don't understand why someone gave me his number. There is much he doesn't tell me, but I still trust him with my life."

"What type of powers does it have? Where is it from? What species?" Doctor Gustav asked trying to move this along. She needed to know how much of a threat this Doctor was before it woke up.

"Powers?" Clara had to think for a minute. She didn't have to lie about anything since the Doctor hasn't done anything to her knowledge that she would need to lie about. She just hoped she wasn't betraying the Doctor by answering truthfully. "Well I guess his kind can live for a long time. He told me he was over a thousand years old. I think he is telepathic to a slight degree. I mean I don't think he can read my mind if I am on the other side of a room, but um yeah..." Clara trailed off at the end since she wasn't sure what more to say about that. "He is the last of his species since his planet was destroyed. He hasn't told me much about his home planet except that it was destroyed during a war. I guess his species would be Time Lord."

"That has all be very helpful," said Doctor Gustav making another note on her clipboard. "I have just one more question. What is this device?"

"That is a sonic screwdriver," responded Clara who saw the object that the scientist was holding. " It is a screwdriver, but it is sonic. It is kind of an all purpose device, but it is non lethal and not a weapon in case that is what you are thinking."

"That is all I needed to know about the Doctor for now. I am curious as to why it brought you here to look for Kal-el. That thing is one of our newest specimens. It has only been here for a couple of months now. Why were you looking for it?"

"I don't know," said Clara. "All the Doctor told me was that the future was in trouble if we did not release Kal-el."

"So this was a rescue mission," said Doctor Gustav. "We already know that they are not the same species so why would the Doctor come here for Kal-el?"

"I told you what the Doctor said," said Clara. "You just can't believe that there are beings out there who want to help us and others. Not everyone is only out for themselves. Will you quit referring to them as things and calling them it? That is very rude."

"I think we are done for now," said Doctor Gustav who proceeded to gather her notes and leave the room. Her next stop was going to be to visit the Doctor. Thankfully she had already witnessed the fact that this specimen could speak English. This would make her job a lot easier since the majority of their specimens could not speak English. She had also gotten lucky with Kal-el, but that creature refused to give her any information.

Soon Doctor Gustav found herself in the same wing as the Doctor and Kal-el. This could be an opportunity to learn more about Kal-el since the Doctor seemed to know of Kal-el and they were near each other. Of course the area was monitored at all times.

"I have a few questions for you, Doctor," said Doctor Gustav to the creature who was sitting on the ground against the back wall of his cell. The doors were see through, but made from a heavily reinforced plastic.

"Ask away," said the Doctor is a cheerful voice.

Doctor Gustav was taken back by his happy tone, but decided this was all an act to get her to lower her defenses. "What are you doing on this planet and what are your intentions for the creature Kal-el?" We know you came here to release it. How many times have you visited Earth?"

"Well I am sure you have spoken to my companion already, so you probably already know that my planet was destroyed. I have kind of adopted Earth as a second home. I have been to this planet more times than I can count over the years. Kal-el is supposed to be a great hero and he can't do that while he locked up in here. I came here to set the future back on the course it is supposed to go."

"How do you know what the future is supposed to be? Are you psychic?"

"I have been to the future and Earth will not reach its golden age if Kal-el remains here. I can feel the Earth moving all around me and I can tell what is supposed to happen and what is never supposed to happen. That was the gift of my people, but now that I am the only one left it is up to me to right the wrongs."

"What was Kal-el doing when you found him?" The Doctor was suddenly very interested in the answer.

"Kal-el was in Metropolis wreaking havoc with its powers."

"Was he wearing any type of red jewelry?"

"It was wearing a red ring. We took it down with the green meteor rock that seems to be its one weakness and we removed all possessions including the ring when it was brought in."

"That red ring was red meteor rock which has a very different effect on Kal-el than the green meteor rock. Kal-el would have reverted back to his usual self the moment the ring was removed."

"Do you know why these meteor rocks affect this creature in such a way?"

"First off, I am not going to answer any more questions until you stop referring to non humans as things, creatures, or it. However, I will tell you that Kal-el has been here ever since his planet was destroyed when he was a baby. He was raised as a human and didn't even realize he was an alien until his adoptive parents told him a few years ago."

"I'll let you get settled in while I go check on a few other subjects. We are not through."

A few minutes passed after Doctor Gustav had left before either Kal-el or the Doctor dared to say anything. Kal-el had of course been listening in to the entire conversation and wondered how someone knew so much about him.

"Kal-el, I am sure you are wondering how I know so much about you," began the Doctor who was speaking to the man in the cell across from him. They could both clearly see each other and the Doctor could see that Kal-el had not been treated well since he had arrived here. He could see a faint green glow in Kal-el's cell and could see handcuffs that gave off the same faint green glow around his wrists.

"How is it that other aliens always seem to know more about me than I do?"

"I met you a few times in the future," said the Doctor. "I know who you really are, but I thought it would be best to leave your human family out of this. I came here to rescue you, but you can see how well that worked out. We can't really say much since we are being monitored."

"It is just nice to have someone to talk to who is treating me like a person," said Kal-el sadly. "I hate how they are treating me like I am nothing. This is why my parents were always afraid of my secret being exposed."

"Do you speak Kryptonian?" The Doctor suddenly asked.

"The Kryptonian knowledge was downloaded into my brain. I can read the language with

no problems, but I have never had anyone that I could talk to in the language."

"I happen to speak every language," said the Doctor. "We can communicate in Kryptonian without them knowing what is being said."

"That sounds perfect," said Kal-el.

"Are you able to understand what I am saying?" The Doctor asked switching from English to the Kryptonian language.

"I can!" Kal-el exclaimed also in Kryptonian.

"Clark, I can't tell you how sorry I am that you are here. You are still just a kid and one day you are going to grow up to be one of the greatest heroes ever. Do you want to talk about what happened in Metropolis?"

"I am so reserved all the time and keep everything to myself. When I get infected with the red Kryptonite I tend to go a little crazy. I lose all my inhibitions and do everything I ever thought about doing. Last time I got infected like this was when I had just accidentally caused my mom to miscarry when I blew up my spaceship. I put the ring on and ran off to Metropolis. This time was different. I have been working at the Daily Planet in Metropolis and spending my time as the Blur saving the city. They say I was wreaking havoc on the city, but that is not true. Okay I might have done a few illegal things. Apparently I like to rob from ATMs and go out and party. I was being a bit too free with my powers and having fun. I even managed to fly which was exhilarating. I can't believe they caught me when I was just floating around. I did try to fight back which maybe didn't them the best impression."

"That all doesn't sound too bad. I've stolen from ATMs while not being affected by anything. Saving the world is pretty much a full time job except without the getting paid part. In my defense, I only steal when it is necessary to saving the world."

"That is probably better than using the money to buy fast cars and party. I swear if I get out of here I will never do anything illegal ever again. It doesn't seem likely that we will get out."

"Clark, we will get out of here eventually."

"How do you know?"

"I am not sure if you know this, but you have the capability to live for a very long time. So eventually we will get out of here."

"What about you?"

"How old do I look?"

"I would guess you are around 30."

"I am over a thousand years old. My kind can cheat death by regenerating. Everything about me changes. This is the eleventh appearance I have had. I used to look like an old man back when I was young. I have looked like this for around 300 years or so without much change. So we both are going to eventually get out of here. Hopefully it is sooner rather than later. I am worried about my friend who they captured. I am not sure what they will do to her. She is human so she should be fine, but that doesn't stop me from worrying.

"Does your human friend know that you're an alien?"

"Of course. The secret is usually out of the bag when I show them the TARDIS which stands for Time and Relative Dimension in Space. She is my ship. I never hide the fact that I am an alien unless I have to like when I was trying to get in here to help you escape."

"Aren't you ever afraid how people are going to react to finding out you're not from around here?"

"I didn't grow up on Earth," began the Doctor. "Your situation is much different from mine. There are people who have always thought you were human. I do think that you need to trust more people with your secret. Your best friends will stick by you no matter where you are from. I understand that you still want to have a normal life. I have never had what you would call a normal life so I don't really need a secret identity. I also don't have cool powers like you do. Eventually you are going to have the coolest costume. No one ever lets me wear cool things. All of my hats get shot off and my bow tie gets ridiculed constantly. Humans just have no sense of taste. What is cooler than a bow tie and a fez?"

Clark smiled at the Doctor's antics which made the Doctor smile in return. He figured Clark hadn't done much smiling since he had been locked up in here. The Doctor let his smile fall when he saw the scientist he had spoken to before returning.

"You will cease speaking in that awful alien language. We know you can both speak English and you will do so if you do not wish to be punished."

"Oh, but Kryptonian is such a beautiful language," said the Doctor who had switched back to English by this point.

"You will tell us what was being said," demanded Doctor Gustav.

"I was just telling Kal-el that some humans have no sense of fashion. I was saying that nothing is cooler than a bow tie and a fez. Much to my dismay, my human friends don't seem to think that I am very fashionable. Speaking of human friends, where is Clara?"

"If you mean the girl you brainwashed, she is doing just fine," said Doctor Gustav. "We are currently working at undoing the brainwashing that you did to her."

"Am I not charming enough that I could get friends without brainwashing them? Kal-el , am I that unpleasant to talk to?"

Clark remained silent. He wished he had the Doctor's confidence, but he had suffered too much already in this place. He didn't want to be punished anymore for speaking out of turn. He figured he would already be punished later on for speaking in Kryptonian.

"Maybe I need to work on my people skills more," said the Doctor as an afterthought.

"Why did you take a human traveling with you?" Doctor Gustav was curious as to why an alien would show a human various parts of the Universe.

"I just like to show others the wonders of the Universe. Originally my grandchild traveled with me, but then I dropped her off when she decided she wanted to get married. I have traveled with various humans throughout the years. They travel with me for awhile and then they get on with their lives. I have also traveled with other aliens. I used to travel with a woman from my home planet and I traveled with a teenager from e-space. I also used to have a robot dog."

"Has anyone died while traveling with you?"

"Unfortunately a few have," said the Doctor sadly.


"Adric, the one who was from e-space was captured by Cybermen and died when their ship crashed. There was nothing I could do. Then there was my human mother and father in law who were sent back in time by the Weeping Angels. I could never see them again, but they were together and lived to be quite old. Finally there was my wife. We kept meeting in the wrong order. The first time I met her was the last time she met me. She died to save my life and the lives of many others. It is difficult living each day getting to know someone and always knowing exactly when they are going to die. Does that answer your question?"

"What do you mean by meeting in the wrong order?"

"I thought that my being a Time Lord would have given you some hint. I can travel anywhere in space and time. My people were the guardians of time."

"Can you tell me about the Time Lords?"

"That lot were quite stuffy and always had this no interference policy. I was always interfering anyway and left my planet because I did not agree with their policies. I also wanted to get out and see the Universe. I was only a couple hundred years old when I left and was still quite the child. They tried to get me to do their bidding since they could then deny any involvement. They did some terrible things that I wanted no part of. I was the one who stopped them. They are all trapped in a time lock right now that hopefully will never be broken. They were brilliant, but they were getting a bit too full of themselves and needed to be stopped. I like to think of myself as the protector of this Universe and as the protector of Earth. I wish you would believe me when I say I would never do anything to harm this planet. This place has felt more like a home than Gallifrey ever did, even though I do find it quite difficult to stay in one place for any long period of time."

"You have been a lot more forthcoming than Kal-el if what you have told us is true."

"Well I don't have as much to lose as Kal-el through being truthful. His whole life could be destroyed. Plus there is the fact that he grew up here. He may have special powers, but he is basically a human who just has some additional abilities."

"How was he able to speak Kryptonian?"

"Doctor, let me answer this," said Clark. "There is an AI of my birth father that downloaded the Kryptonian language into my head. He wants me to go through training to learn more, but I have have been refusing to for years now. It was only recently that I realized I had been misunderstanding Jor-el since the beginning. I thought he was implying that it was my destiny to conquer this planet and rule it with strength and I refused this every step of the way. Only recently did I come to realize that he sent me here to set an example for others and to be a symbol of hope."

"See I still think that you are here to conquer the planet and that you were placed here as a child to learn our ways and report back to your people."

"Even if that were true, I love this planet and I love my human parents and my human friends. If that was Krypton's plan all along, than they failed. I would never betray this planet. I have even fought off others from my planet to save this world."

"What were you doing in Metropolis when we found you?"

"I was infected with red Kryptonite which takes away my inhibitions. I was partying and having fun with my powers. I never hurt anyone. I was just being a bit reckless, but that is not who I am when I am in my right mind. When you found me all I was doing was floating around. I had just started to learn to fly and was enjoying the feeling of floating. It is not like I was doing anything destructive when you took me down."

"I see that having the Doctor around has made you more confident and chatty," said Doctor Gustav. "I guess it is a good thing we put you two near each other. Kal-el it is almost time for your daily session. Doctor, we will begin with you tomorrow."

"Just leave him alone!" The Doctor yelled. "We have both been forthcoming with you. Can't you just leave him be?"

"Getting it to talk was just one of the things we wanted. So much more can be learned through experimentation."

"We'll be seeing you later, Doctor," said Doctor Gustav with a smile. Guards showed up and pulled Kal-el out of his cell and took him away leaving the Doctor slumped against the wall, powerless to stop what was about to happen.

A/N: Here is the end of chapter 1. This chapter was mainly an introductory chapter to get everyone to know the Doctor and Clark. Next chapter will be taking place in the past and will be from Clark's perspective. I appreciate all that read, review, follow, favorite...