Wake Me Up Inside – Chapter 3

Title: Wake Me Up Inside

Author: Thothkristen

Fandom: Stargate Atlantis/Stargate SG-1

Relationships: John Sheppard/Evan Lorne, Carson Beckett/Radek Zelenka, Rodney McKay/Ronon Dex (eventually), Markham/Stackhouse

Genre: ShapeShifter (Mythological Creatures and regular animals), Angst, Alternate Reality

Rating: MA (more for the future chapters)

Warnings:  Flashbacks/dreams of past verbal, psychological and physical child abuse, angst, m/m sex, explicit language, violence, explicit sex, brief mentions of past torture and kidnapping

Word Count:  7,318/ 35,000  (This update is 1, 650)


The next morning, SGA-1 decided to convene in the armory. While they were hopeful that they would not need to guns, they decided that they should be prepared for the worst possible outcome.

As Rodney was double checking that he had the right information on his tablet and his ZAT working properly, he noticed that the smells from the day before were lingering nearby. He allowed himself to breathe in and out a few times. Just like yesterday, the smells made him feel relaxed and safe.

He tried to make himself more aware of his surrounding to see if he could figure out where the scent was coming from. All he could hear was Ronon and John entering the armory. From being around John so much, Rodney knew that his smells were cordite and salt water. Even though Rodney’s sense of smell was a bit more sensitive than it was before he first shifted, he did not personally go around smelling people because that would be rude.

When Ronon and John got closer, Rodney took another deep breath and realized that smells were coming from Ronon. Shit. Fuck.

Rodney tried to change his thoughts because there wasn’t anything he could do about it for now. He knew that this trip to the West Tower of Atlantis had to be at the forefront of his mind to make sure that nothing happened to anyone of them.

In addition to SGA-1, they decided to bring Sgt. Markham, Sgt. Stackhouse and Dr. Jarod Miller along. Rodney figured having another geek along would help, especially if they come across some more Ancient Tech.

Upon seeing the new scientist, John took in the appearance of the newest member of Rodney’s science team. Dr. Jarod Miller was probably about six foot tall with dark hair that was styled in a proper way. He had brown eyes that were the color of chocolate. He had come out to Atlantis on the recent Daedalus run. Dr. Jarod Miller came highly recommended for his knowledge of the Ancient language and Ancient Tech because his ATA gene was quite strong.

Once everyone was set, they moved towards the west tower. They ended up taking the transport to the level that Rodney knew that the two rooms would be located. Shortly after they exited the transport, Rodney started to hear a humming noise followed by some blinking lights.

“Are you playing human light switch, Sheppard?”

“No. Well, I don’t think so. I didn’t do anything intentionally.” John responded.

“Hmm…” Rodney said absently as he looks at his pad. He notices that there a lot more fluctuations going on with Atlantis but he doesn’t see the cause of it.

Deciding it was safe, Rodney led everyone down the corridor to where they came across two set of doors that looked like they opened up to the two possible rooms.

One set of the doors whooshed open and the lights seemed to be slowly rising to full power as they were entering the room.

“Is this your doing, Sheppard?”

“No, I—“

“Actually, I did it, Dr. McKay.” Dr. Miller said from the side. Everyone turned to look at Dr. Miller.

“How?” Dr. McKay asked.

“Before we entered, I noticed a side panel. I was able to take an educated guess on which ones would be for the lights.”

“Where? I didn’t see any panel.”

Rodney went back into the hallway and did actually notice the side panel this time.

“Huh.” Rodney took a look at the panel to see if there is any other buttons or things that might be useful to the science team. Seeing nothing that was obvious, he went back and joined everyone in the room.

When the lights finally came up, everyone took a look around the room. Rodney noticed the high walls on all sides of the room, with tall windows on one of the sides that look out to the ocean. On another side, it looked like a small platform that jutted out over the floor. When Rodney looked up, he noticed that it looked the ceiling might partially or fully open up. He was beginning to wonder how he might be able test out the theory when they started moving on their own.

Rodney started looking around and no one seemed to have an answer for him. Rodney glared at John but he held up his hands in placating gesture.

Before Rodney turned around to take a better look of what the room looks like, his mind was inundated with images. Rodney brings a hand to his temple and started to gently rub it.

“Rodney, are you alright?” John asked in a soft tone and started to head towards Rodney. John knew that Rodney suffered from headaches from time to time.

“I’m…..Yeah. I think.”

“You are not giving me a vote of confidence here.”

After a few minutes of quietness, Rodney finally spoke softly, “Sorry. Apparently, this room was used by the Ancient shifters.”

“Ancient shifters?” John queried.

“You mean the Ancients from Atlantis?” Dr. Miller asked.

“Yes. Apparently, this was their meeting room and/or hanging out room.”

“How do you know?” Dr. Miller asked with a slight frown on his face.

“I just know. Images appeared in my mind of what went on with this room.”

“Images? Is Atlantis talking to you?”

“I-I—think so.”

“She hasn’t before?”

“Beyond the querying of her databases and occasional e-mail, no.”

“Are you feeling alright?”

“Besides an endorphin rush and heart racing, I’m doing alright. Slight headache too. It was quite unexpected.”

“Was it standstill images or something else?”

“It was somewhat of a mixture. I actually now know how to make this room exactly like that used to have it. We might want to change a few things but I know about some of their cubby holes and there is a bathroom off to the side over there.” Rodney reached out and pointed to the far corner where a door was starting to open.

“Atlantis is just talking to you, not in your mind controlling your thoughts?”

“No, I’m not a pod person. She hasn’t talked to me before.”

John, Rodney and Jarod walked over and peered into the room. It was a decent size bathroom with a shower in it.

“This bathroom will be useful for the shifter hangout/meeting room.” John commented. The room was huge, so he guessed that there were either a lot of Ancient shifters or they might have shifted into large animals.

“Can you make it look like it was before?” Dr. Miller asked in a curious voice.

“I-I think I can.” Rodney attempts to access the information on his pad but nothing happens.

A few minutes later, the ceiling doors closed again. Shortly afterwards, an image of woman with long brown hair and blue robe appeared before the team.

“Good morning, Dr. McKay and Colonel Sheppard.”



“Why are you here?”

“To be useful to the Keeper of Knowledge.”

“Who is that?”

“The dragon always protects Atlantis’ knowledge from getting into the wrong hands.”

Upon hearing the words, Rodney muttered, “Me”


“But why?”

No response from the image. If anything, the image seemed to have taken on a ‘are-you-kidding-me’ look.

Realizing that he wanted an answer, she said, “You made me come alive again. You take great care of me and understand me.”

Rodney blushed a little at the compliment.

“You are amazing. Of course, I would take great care of you. I am honored by the title.”

“It comes with responsibility.”

“I understand.” Rodney was not going to turn down this opportunity. He loved Atlantis and all that she offered.

“What do you need?”

“Can you make the changes to the room to make it look like it used to?”

Right before their eyes, platforms were rising from the floor and coming from the wall. Soon, there was a nice sitting area and tables to place things on. Upon further investigation, they noticed that near one of the corners that the floors were heated and cubby holes on two of the walls.

“Atlantis, can any of the flooring be heated or is it just this corner?”

“Any. You will need to let me know.”

“John, do you have a preference?”

“For now, why don’t we keep to the heating the corner area. I’m sure we can change it in the future if we want to.”

“True. Any other requests?”

“No, I think we are good for now. The room will do very nicely for the pride.”

“I agree.” Turning back to the image of Atlantis. “Thank you for your help. Can I call upon your image anywhere on Atlantis?”

“Yes. Just call my name and say appear. I will be there right away.”

John muttered, “And here I thought I was the Golden Boy.”

In a louder voice, “Thank you for your help, Atlantis. Can I call upon your help too or do I still need to go to the control chair?”

“I can appear too for you. You are the Protector of Atlantis. The griffin always protects Atlantis, while the dragon protects the knowledge.”

“Protector of Atlantis?”

“Yes. Do you not want the responsibility?”

“No, I do it anyway. I just hadn’t realized that you knew or gave me a title.”

“Colonel Sheppard, Dr, Mckay and Arianya are all very special to me. If I can help it, no harm will come to any of them.”

“Thank you, Atlantis.” John and Rodney said at the same time, not entirely believing their ears.

“If you have no other use for me, I will let you be.” Atlantis responded.

“Actually, could you help us go through the room across the way?”

“Yes. I will meet you there.”

Atlantis’ image disappeared.

Everyone looked at each other in disbelief. They have never had Atlantis appear to them in this form before. They hope that this bodes well for the Lanteans.

About thothkristen

I love writing slash fiction, especially if it deals with shifters and mythology. I use my Wordpress account for Writings in Progress and my Archive of Our Own Account for when a work is completed and has been betaed.
This entry was posted in Naked Nano, SGA/SG1, Shapeshifter, Wake Me Up Inside. Bookmark the permalink.

12 Responses to Wake Me Up Inside – Chapter 3

  1. ElfQueen says:

    *shakes pom poms* Atlantis is alive!

  2. gail19 says:

    McDex sounds like it’s a McDonalds but only serves hot men – as in you have to be a hot man or thats where you go to order one? ; }

  3. Atlantis being sentiente and projeting herself is amazing.
    Mcshep friendship being the 1th line to protect and know Atlantis is real great

  4. greywolfthewanderer says:

    woo hoo hoo!! *bounce, grin* this is soooo cool!

  5. AI Atlantis one of my fav AU.

  6. how does one get to chapter one? thank you

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