The Atlantis Project

Rating: K+

Disclaimer: Okay I do not own any of the characters they are owned by MGM, and DC Comics

Parings: Stargate Atlantis: Elizabeth/John, Teyla/Aiden, Jennifer/Ronon, and Katie/Rodney

Smallville: Chloe/Clark, Lois/Oliver, Tess/Lex, Lana/ Pete, and mentions of Lois/Clark, Chloe/Oliver

Summary: A mysterious ships lands in the fields of Smallville, Kansas. Martha Kent discovers the ship and takes the mysterious stranger back to the farm. This mysterious stranger is Dr. Elizabeth Weir who disappeared in the Pegasus Galaxy however she has a tie to the Kent her and Martha were college roommates. Bonding with Martha Kent again she meets Clark Kent who is now Superman in Metropolis. One more thing Dr. Elizabeth Weir is the aunt of Chloe Sullivan who is now working on Atlantis off of the coast of San Francisco, California. Chloe Sullivan left the life she used to live behind to put the past in the past. The return of her aunt may lead her back to her old life when she needs it the most.

The Atlantis Project

Prologue: Smalliville, Kansas 2015

It was nightfall when Martha Kent was driving along the corn fields when she saw a flash of smoke shooting across the sky. Martha pulled to the side of the road got out and followed where the ship landed. Once she got there she noticed that the ship was Kryptonian and that a woman was lying on the ground. Once she got close enough she noticed the woman as none other than Dr. Elizabeth Weir who was well known in Washington and went missing seven years ago. Another fact was this woman was also her college roommate back in the day. After a few minutes the woman started to stir and noticed Martha.

Elizabeth: Martha?

Martha: Yeah. Come on I take you back to my place and we can talk some more.

(Martha helped Elizabeth up and they picked up the ship. Once they got it in the truck they headed back to the Kent farm. )

Elizabeth: I can't believe I am seeing you again and I heard several years back that you became Senator Congratulations.

Martha: Actually it was Jonathan my husband who one but he died of a heart attack before taking office.

Elizabeth: So natural they asked you to take his place.

Martha: Yeah that pretty much is it. What about you how did you end up coming into the atmosphere in a Kryptonian ship?

Elizabeth: That a long story and how did you know it was an alien ship?

Martha: Well I can't wait to hear the story. You'll be surprised how I know. Well were here why don't you get cleaned up and we'll talk later.

(Elizabeth and Martha got out of the truck. Before Elizabeth went to clean up she helped Martha move the ship into the barn cellar so no one could see it. It was an hour later when Elizabeth was ready to talk. She came down stairs into the kitchen looking around the place.)

Elizabeth: Well Martha I can say this is a pretty place you have?

Martha: Thanks Elizabeth actually it Jonathan's family farm.

Elizabeth: Wow it you have kept it up this long.

Martha: Actually while I was in Washington my son Clark has kept it up.

Elizabeth: I seem to recall that you and Jonathan can't have kids.

Martha: We can't but we adopted him. To answer your question about the ship earlier Clark is the reason I know about Krypton.

Elizabeth: You telling me your son is an alien. That explains some of the letters I got from Chloe Sullivan before I went missing.

Martha: How do you know Chloe Sullivan?

Elizabeth: Oh right I never told you I have a half brother and she just so happens to be my niece.

Martha: You Gabe Sullivan is your half brother and that explain some of the mannerisms she had reminded me of you.

Elizabeth: She was always my favorite niece how did you think became a master of words.

Martha: Yeah it always stumped my son with the way she could twist words around.

(Just then the door opened revealing Clark walking through the door greeting her.)

Clark: Hey mom what with the new Kryptonian ship in the barn cellar?

Elizabeth: Clark I presume I can explain that I am the reason it is hear.

Clark: Excuse me and you are?

Martha: Clark I like you to meet Dr. Elizabeth Weir who happens to be my college roommate back in the day.

Clark: You mean the girl you did all the crazy things with in those pictures?

Elizabeth: Martha you showed him those. Yes Clark I am her and it seems that you know my niece Chloe Sullivan.

(Clark shook her hand but Elizabeth noticed that at the mention of the name the light in his eyes disappeared. Clark excused himself to the loft in the barn. Elizabeth did not know what to say.)

Martha walked over to her offering some coffee and said let him be. Then Martha guided her to the living room so she could share her story. They sat down and that is when Elizabeth noticed all the pictures around. Martha, Clark, and Jonathan and next to it was a picture of Chloe, Clark, and Pete the early days also she noticed Lois crouched down with a dog. Martha was patiently waiting for Elizabeth to speak. Martha would wait all night because she could not imagine what her former friend has been through.

Half an hour later, Elizabeth finally spoke but first apologized for whatever she said that offended Clark.

Elizabeth: Look Martha I am sorry for whatever I said that offended your son.

Martha: It quite all right it just things did not end well for them and my son blames himself for what happened between them.

Elizabeth: Ok I understand where is she now?

Martha: No one knows she just disappeared. Anyway I want to hear your story.

Elizabeth: I guess I put it off long enough but a lot of what I am going to say is classified military stuff. I have a feeling I can trust you not to tell anyone and then there is something I need to tell Clark.

Martha: You can trust me.

Elizabeth: I guess when you were in Washington you heard that I went missing in action but not from what. Well for sometime in Colorado Springs in a Cheyenne Mountain base the military was running a program called Stargate program. This program allowed for us to do planetary travel well they had been doing this program secretly for seven year before I heard about it. When President Henry Hayes was elected wanted to make this program public that's where I come in. He appointed me to run the program for three months.

Martha: You work for the military you were always against it?

Elizabeth: Yeah I know but how do you say no to the president and after reading the reports of the missions I was amazed so I did the run. However three months later they appointed one of the military leaders to run the Stargate Command and I was asked to head up this new project. This project was part of this program to create an expedition of scientist and researchers at an outpost and that when they discovered that there was possibility to find the Lost City of Atlantis. I know the myth but it does exist we found it but in another galaxy. So I headed the expedition out there that where I have been.

(Just then Clark came back in to apologize and sit join his mom.)

Clark: Sorry Dr. Weir for leaving abruptly like that it just Chloe is a sore subject for me.

Elizabeth: Please call me Elizabeth and I understand my niece can leave a lasting impression.

Clark: Niece?

Elizabeth: Her father is my half brother Gabe and I have the same mother. Anyway I was just telling your mom how I ended with that ship.

Clark: That I like to know too.

Elizabeth: Good because I have something for you. Anyway we found the Lost City of Atlantis in the Pegasus Galaxy and for a year we had no contact with Earth. The gate from Earth had enough power to make a one way trip. A year later we found another power source and made it back to Earth. We were in danger of losing that city to an enemy that fed on humans by taking their life force. Along the way we ran into another enemy that at first we thought was the original creators of the gate but we were wrong they were machines. The machines were created in the image of the gate builders so looked so human. What makes them function are little machines called nanites and one infected me as we were trying to escape their hold. So I was infected and when active they create a link to the machines. We were able to keep them dormant for a while until I was badly injured and the only way to keep me alive was reactive them.

Clark: What happened after they reactivated? Before you continue I heard the beginning of the story and you can trust me too.

Elizabeth: I know I can. Well we were in space heading toward a new planet but need more power to run the city. So using me a decoy to distract the machines to get the power source it worked however the machines caught on and I had to sacrifice myself to save the team. So I was in the hands of this enemy but before I got in there hands we discovered the machine were made to fight the other enemy and we reactivated that program. Well I was hands of the enemy a renegade faction wanted to just live in peace and not fight anyone. I joined this faction we were on a space ship hiding I also discovered that Atlantis found a way to destroy this enemy planet. Over time we fought the wraith and trying to be in peace. After a while our ship was attack and I landed on the planet and somehow survived. I figured since the machines deactivated my human side save me. On this planet a blond haired girl found me nurse me back to health. She was to pull the nanites out of my system with a piece of their technology. As I healed after that Kara told me of her race.

Clark: My cousin Kara.

Elizabeth: Yes Clark she told me of the Kryptonian race and she fine. She is safe and she is the one who helped me get back here. She must have programmed the ship to take me to here because she knew I be safe. She wanted me to give you this letter.

(Elizabeth gave him the letter and then finished the rest of her story.)

Two hours later Elizabeth finished her story. Martha got the guest room ready for Elizabeth to stay and get some rest. Clark went up to his old room and stayed overnight.

The next morning Elizabeth got up to the bright sunshine and then headed downstairs. She found Martha downstairs preparing breakfast and had a pot of coffee ready. Elizabeth got a cup headed over getting some coffee. She smelled it taking the sweet aroma in Martha noticed and smiled.

Elizabeth: Martha what is that smile about?

Martha: You just reminded me of your niece and how she loved coffee.

Elizabeth: I think I got her addicted to it when she was ten and over at my house visiting.

Martha: Ten really well she did her best work on the stuff in high school.

Elizabeth: Also another thing I noticed is that you know Lois Lane also in some of the pictures.

Martha: Is she your niece also?

Elizabeth: No but I have met her because Chloe and her were always getting into trouble. The reason I am asking is I am surprised to see her pose with a dog.

Martha: I take it she was not a dog person but Shelby was special.

Elizabeth: No my dog knew not to mess with her but why is yours so special?

Martha: Funny story how we ended up with her Lois accidently hit the dog and felt so bad took her back here to the farm. This was despite her allergies and we hope to find it owner however the dog was part of experiment. In the end the dog got better we ended up with Shelby.

Elizabeth: Now I see Lois always had a good heart. Anyway where is Clark?

Martha: He is doing Superhero duty in Metropolis and then be back.

Elizabeth: Right Kara told me about the Red-Blue Blur. That is a mouthful whoever gave him that name.

Martha: Yeah it was and it was a dear friend and your niece's dead husband who gave him that name. Anyway you are a few year off now he Superman these dubbed by Lois.

Elizabeth: That does sound like Lois but I am surprised it wasn't Chloe who gave him that name.

Martha: That because Chloe disappeared before Clark became Superman.

Elizabeth: You mentioned that Chloe had a husband he is dead what happened?

Martha: That you have to ask Clark about because that part of the fallout they had. Anyway what are you going to do know that you are back?

Elizabeth: I guess I have to head back to Colorado and alert the military and everyone I am back on Earth and no longer a threat. I like to take Clark with me so I have proof I landed here.

Martha: I think he have no problem with that.

(Just then Clark appeared in the Superman uniform and Elizabeth had to keep from laughing.)

Elizabeth: How can someone name him Superman in an outfit like that?

Martha: Hey watch it I made that outfit. Anyway since he does not like masks it keeps the attention off his face.

Elizabeth: Sure does. Anyway Clark I wanted to ask you a favor.

Clark: What is it?

Elizabeth: I was wondering if you like to come with me to the Stargate Command in Colorado so I can explain how I came back to Earth.

Clark: Sure I could use a vacation with and away from Lois bride to be.

Martha: Oliver proposed.

Clark: Yes he did.

Elizabeth: Lois Lane engaged crazy I see things have really changed with her. No I am not her aunt but with Lois and Chloe being close I got to know her.

(Clark had a smile on his face and then went to make the call to Perry.)

Elizabeth just smiled back and watched him leave to pack. Then she went over to Martha thanking her for the hospitality and waited for Clark to come down. When Clark came down with his bags Elizabeth picked up her jacket and the one bag of clothes she had they headed out to his truck. Clark opened the door for her and she gave him direction once he got into the driver side and they headed off to Colorado where Elizabeth is going to meet her friends again.

Here is a new story that came up in my mind. I am a big Dr. Elizabeth Weir fan and currently I have been writing a lot of stories for Smallville but thought I make this one a cossover. Enjoy and Review.