Hi everyone! As always thank you to everyone who has alerted and favourited and reviewed my story, it means so much to me knowing that people are reading and enjoying! In this chapter there is a bit of medical knowhow, I am no doctor or nurse and I probably never will be so if something is wrong or doesn't add up don't hang me out to dry please! This is a fiction story anyway so some things can be made up, but hopefully i've kept it very doctor professional! Also in this chapter is a bit more interaction with more characters, and we're moving on in the episodes! More interactions with our favourite flyboy, but don't be expecting something to happen for a little while longer, that will be coming I promise and I will not disappoint. Enjoy and let me know what you think about the chapter!

Breaking Ranks - Genesis

I shrunk back down into my chair, ok, maybe I had been reading for far too long, and as much as I hated to admit it; I was pretty fascinated with the ancient technology. Sighing, I stood and took my tray to the bin as Major Sheppard handed the tablet to me. I thanked him as we walked out of the mess hall and towards the military living quarters.

The halls were dead quiet and completely empty as we walked down them, that was until I started talking. "I just want to clarify that my actual job in the army wasn't just building tanks and rockets," Sheppard glanced over at me, "If there had been an accident regarding machinery it was my job to find the fault and repair it so it wouldn't happen again. And when I was stationed out in Afghanistan I helped repair damaged vehicles and weapons that had been damaged in the war."

"So you never actually fought in the war?" he asked as I nodded my head.

"Oh god yes. I was a soldier long before I became a mechanical engineer. I enlisted when I was seventeen and they put me in the advanced hand-to-hand combat and artillery training. As soon as I was ready they shipped me off. I only finished my studies about a year ago."

"Oh." Was the only thing Sheppard said. I chuckled to myself as we reached the door to my quarters. I went to wave my hand over the device when a thought popped into my mind and I just had to ask Sheppard.

"Major, can I ask you something?" I asked as I turned slightly to look at him. I saw Sheppard shove his hands into his pockets.

"Shoot."

"Why are you doing this?" I said. I could see on his face that I had caught him off guard with my question. He didn't reply so I continued, "Why are you being so relaxed and nice to me?"

"I'm always like this," he said, trying to give a smirk.

"No, you're not. It's because of him, isn't it? My dad." I saw his body tense up and I knew I had hit the Hail Mary. "Clearly everyone thinks that I am incapable of taking care of myself."

"No one thinks that—"

"Really? Because I've been saying it for days and every time I'm around someone they look like they're walking on eggshells, like I'm going to break down or something. But here's the thing. Colonel Sumner may have been my dad, but he was never there for me. He stopped being my dad when he turned his back on me for joining the Army and not his beloved Marine Corp. The photo that you found in his jacket, my first day of High school, that was the only day I saw him that whole year, not for my birthday, and not for Christmas. He only came because it was a school run by an ex-marine. Get it now? My dad only wanted me so that I could follow in his footsteps."

"He was still you dad."

"So what if he was? He was more of a dad to Ford then he ever was to me." I moved my hand over the door device as it opened. "I don't need anyone to look after me, Major Sheppard, I've been doing fine the past ten years. Goodnight." I said as the door slid shut. I watched his shadow walk away as I headed over to the desk and saw the dog tags and picture. Opening up the small drawer I dropped them both in and slammed it shut.

I showered and changed into a long green shirt and finally let my hair down; I was just about to settle down into bed when the door sounded. I sighed and went to ignore it, "Mia, its Ford. There's an emergency." He sounded serious as I hurried over to the door and moved my hand over the sensor as the door opened and Ford stood there in his full gear.

"What's happened?" I asked immediately.

"Jinto's missing. We're going in teams of two to search the city. You're with me." He said as I nodded and rushed to grab my clothes. I quickly changed into my trousers, boots and tight black shirt. I pulled my hair into a high ponytail as I opened the door as Ford handed me the vest and P-90 as I zipped and strapped. Once I was ready we headed off to the Jumper Bay, as it was our first place to search. "Here," Ford said as he passed me an ear radio. I hooked it onto the back of my ear as I heard voices saying that areas were clear as I tuned it out.

Ford and I searched the Jumper bay but there was no sign of Jinto ever being there. We then made our way down to all the science labs; it was eerily dark and creepy down here. As we walked I had the feeling that we were being watched as a cold shiver ran up my spine as I stopped and turned. I raised the gun as I scanned the area, Ford stepped next to me and whispered, "What is it?" he asked, I could feel his stare on me. I lowered my gun, I was over-reacting, and there was nothing there.

"Nothing." I mumbled as we turned and started walking again. We reached the labs as Ford turned to me.

"We'll split up, there's fourteen labs which are being used and four not being used. So half each then meet up back here once we're done. If you need anything call me on the radio." He told me as he disappeared around a corner. With a horrible feeling in my gut I set off to check the nine labs.

Jinto was a slippery bugger I'll give him that, it had taken me at least near to an hour to search eight of the labs, I had one left which had a naquadah generator in it. As I was walking to the lab the lights and power suddenly switched off as I jumped. I was plunged into darkness as I turned the light on my P-90 on as I scanned the area. I reached up to my radio and clicked it on. "Ford, you got power where you are?" I asked as I continued down the corridor.

"No, I think the whole city's gone dark." He replied through the radio. Just before I reached the science lab the power came back on. It had lasted only a minute but it had felt like hours in the dark and creepy city. I turned the flashlight off, and as I glanced up I stopped in my tracks.

The door to the science lab was open and inside it was pitch black, and it wasn't from the lights not being turned on. It looked like a giant shadow, but smoky. The black smoke was swirling around something in the lab; I could see a faint light which I assumed was the generator, I'd seen a few of them before. Suddenly the power went out again as the light from the generator was gone. My hand went to my radio with a shaky hand, "Ford, the power on where you are?"

"Yeah, I'm back at the meeting point."

"—All teams fall back to the gate room." Sheppard's voice said over the radio. I was still staring at the smoke when I wanted to test out if this thing was alive. I raised my gun and lined it up with the scope. Pulling the trigger quickly the shot rang out and sliced through the shadow.

"Mia!" Ford said through the radio, "Mia what's going on?" I was going to reply to Ford when the smoke began to move out of the room and head straight for me.

"Oh shit." I gasped as I spun on my heel and ran for the hills.

I glanced over my shoulder; it was closing in on me, probably because I pissed it off.

"Lieutenant report!" Sheppard's voice commanded through the radio as I skidded around a corner, at the end of this corridor was a shut door, and I prayed that even though the power was off the door would open.

"I don't know, but I pissed it off!" I yelled into the radio as I reached the door, I moved my hand over the device frantically but it wouldn't open. I turned and pressed my back onto the door as I saw the smoke drawing closer and closer to me, around me the lights flickered back on and the door behind me opened as I screamed and fell back onto the floor as the door smacked shut. I scurried back on my elbows, waiting to see if the smoke came through the door. After a few seconds I heard running footsteps and turned my head to see Ford, Major Sheppard and a few other Marine's coming towards me with their guns raised in defense.

"Mia!" Ford yelled as he appeared at my side and grabbed me by the upper arm and pulled me up into a standing position.

"Lieutenant what happened?" Sheppard said, I ignored him and went straight to the doors; I waved my hand over the console as the doors slid open. I prepared myself to see the black smoke but it wasn't there.

"Lieutenant." I heard Sheppard's voice, stronger and more commanding this time as I turned slowly.

"It was right here," I whispered.

"What was?" Ford asked. I rubbed my head as I met Sheppard's eyes.

"It was this smoke, it was in one of the science labs. I shot at it and it chased me here." I explained. I watched as all the Marine's, including Sheppard and Ford, gave each other skeptical looks.

"I'm not crazy!" I cried, "There was all this smoke, it was draining the power from the generator." They didn't say anything as I looked at Ford, he averted his gaze from me. "Ford, believe me." I pleaded to him. He gave a look to Sheppard as he stepped towards me.

"Mia, you've been under a lot of stress, mostly emotional. Sometimes people imagine things to distract them—"

"I didn't imagine this!" I cried, acting like a child. "This isn't because I'm emotionally traumatized. I'm telling you, this smoke or shadow whatever tried to attack me!"

So they didn't believe me. After my little 'meltdown' or whatever nonsense they spewed out Ford and Sheppard marched me straight to the infirmary to be checked by Beckett. I was lying on one of the beds, my boots off and my hands folded over my stomach as I glared at the ceiling. The curtain had been drawn around me to give me some privacy but I could still hear McKay winging about fainting earlier. As I lay there I heard voices on the other side of the curtain. I sprung up, thanking myself for taking my boots off so that they wouldn't hear me as I walked to the curtain.

"How's she doing, Carson?" that was Weir's voice.

"It's hard ta say. The poor lass has gone through quite a traumatic experience the last few weeks, travelling to a new galaxy, getting captured by the Wraith and having her father die all in the same day would send any normal person over the edge."

"So you're saying she's having a mental breakdown?" Sheppard's voice surprised me; I didn't expect him to be there.

"Not exactly a breakdown, more of a getaway. See, when most patients go through an experience like this it's not uncommon for them to imagine something that represents the pain they are going through."

"So the black smoke?" Weir spoke again.

"Could represent her father dying, or the Wraith for that matter."

"You should've seen her face doc. She looked petrified of the thing. Are you sure its emotional trauma?" Sheppard asked.

"It's hard to tell under these circumstances, but I would like to keep her under observation for tonight, just to be sure she hasn't contracted a virus from one of the science labs."

"Alright, let me know if anything changes." I heard Weir say as I heard her footsteps disappear. I scurried back to the bed and jumped back onto it just as the curtain pulled back to reveal Beckett with his tablet.

"I'm sorry about this, but I just want to keep you here tonight under observation."

"I know Dr. I heard you guys talking, you weren't being subtle." I chuckled as I saw Carson's cheeks flush a little. He placed his hand on my shoulder and squeezed it reassuringly.

"Get some rest, love." I nodded to him as Carson left me alone as I sighed and rolled over onto my side and shut my eyes.

It wasn't long before the curtains were ripped away as I jumped slightly and almost fell off the bed. "Good news Lieutenant, you're not crazy." Major Sheppard said with a smirk on his face. I jumped off the bed.

"I'm not?"

"Nope," he said, popping the 'p'. "Not sure if it's a good or bad thing but Grodin and I just saw the same thing you did."

Beckett came around the corner, a frown on his face, "Major Sheppard, Lieutenant Sumner needs her rest."

"Doc she's not having an emotional breakdown, the smoke she saw is real and is feeding off our generators." Sheppard said as I started putting my boots on my feet.

"Oh." He stuttered, "Well I guess that's good then," he said, shrugging as I stood up straight.

"So can I leave?" I asked, crossing my arms. Beckett sighed and gave me a half smile.

"I don't see why not."

"Thanks!" I said cheerfully as I brushed passed the good doctor and followed Major Sheppard out of the infirmary.

"Dr. Weir want's to speak to you about what you saw, seeing as you're the first one to have a hostile encounter with it."

I chuckled dryly, "I guess that makes me lucky then," I saw his mouth pull up into a smirk as we continued down the corridors at a swift pace.

"Major Sheppard." I began as we stopped at the base of the stairs to the control room. He turned to me. "About last night, or this morning, whatever."

"Don't worry about it, you're under a lot of stress right now." He turned to run up the stairs but I called out.

"Major, please let me explain." I begged as he stopped and looked down at me. "My dad and I had a lot of unresolved issues, but what I said about him, it wasn't true. Even through everything, he was my dad. And I'm sorry about what I said about you looking out for me because of him, I had no right, Sir." Sheppard didn't say anything as he turned and hurried up the stairs two at a time. I collected my thoughts as I hurried up them after him. I came to the control room and saw McKay, Weir, Grodin and Sheppard standing around one of the control panels.

"It didn't look like the phantoms the Wraith make you see, but I can see how the Athosian's would be confused."

"What did it look like?" Weir asked, it seemed none of them had noticed my presence yet.

"It looked like a…"

"Darkness," Grodin said, cutting off Sheppard, "It surrounded the naquadah generator and started to grow like it was feeding off the energy."

"When you shut it down, the whole…whatever it was, it just went away." Sheppard explained to them, though it sounded exactly the same as my own encounter. McKay stepped forwards with a power bar.

"If this thing feeds on energy, we could be in big trouble, and when I say "we", I mean "you," because I wont actually be around for much longer."

"So we need to figure out exactly what it is and what to do about it." At this point I stepped forwards and cleared my throat.

"Well, I can tell you that the exact same thing happened to me just like Dr. Grodin and Major Sheppard." Everyone finally acknowledged my presence as I held my hands behind my back with my chin held high. "When I saw the smoke, it was in the science lab, feeding off the generator, it's why the power was going on and off randomly. Once all the power was gone the thing went for the only energy left in the area…me. I don't think it was bothered by me firing at it, it just wanted more energy and it chased me, until I ran into Major Sheppard and it had disappeared." Weir stared at me for a few seconds; I could tell from her expression that she was feeling guilty about sending me to Beckett because everyone thought I was having a mental breakdown.

"How about if we start shutting off all the generators?" she looked to McKay as he rolled his eyes, "As the good Lieutenant just said, people give off energy, you start taking away the naquadah generators—"

"And it will come after us," Weir sighed.

"Well, I only know one thing for sure, and that is that flying darkness that eats energy can only be very, very bad." McKay murmured as Grodin gave him a glare.

"Okay, we keep the power on. Grodin, figure out a way to detect it, and in the meantime, Major, establish a constant surveillance on all the generators. If one of them is targeted, we'll shut it down remotely. I mean, hopefully we can keep this…thing busy until we figure out a way to get rid of it." Weir hit her radio as she began to address the rest of Atlantis. "Attention, everyone. This is Weir. For the time being, we need you all to remain in your quarters unless otherwise instructed. If you see anything out of the—"

"Hello? Can anyone hear me?" a voice cut into Weirs announcement. I frowned as I recognized the voice as Jinto.

"Jinto?" Sheppard said into his radio.

"Major Sheppard!" he replied with relief.

"Are you okay?" Weir asked him.

"I'm scared," came Jinto's timid reply.

"Where are you?" Sheppard asked him.

"I don't know." He replied.

"Jinto start from the beginning. Tell us how you got to where you are." Weir said as there was a few seconds silence, and then Jinto spoke again.

"I was in the hall outside my quarters." Without anyone saying anything we all rushed off to the living quarters.

We arrived at Jinto and Halling's quarters where Teyla and Halling joined us as I hung back with the two Athosian's as the rest continued on. Sheppard was asking Jinto where he went as he led us to a door that opened, it was a small compartment and when McKay and Sheppard stepped inside a panel opened up that had a glowing map of the whole city. Jinto admitted to touching the map but he couldn't remember what part he touched, McKay announced that they had a weird energy reading from one section as Sheppard touched it. The door closed on them as Weir rushed forwards and waved her hand over the panel. The doors opened again and she frowned back at us when the room was full of crates from Earth.

"It has to be a transporter," I said from Halling's side. Weir nodded in agreement to me as Sheppard's voice crackled through the radio.

"We've got Jinto, he's alright." I see Halling let out the breath he had been holding as he smiles down at Teyla. It was a few minutes later when the doors opened and Jinto came running out and ran into Halling's arms. I stood back as I watched the father and son reunite as they headed off to their quarters, Jinto was rambling on about how scared and sorry he was.

Hope you all enjoyed! So we found out a bit more as to why Mia and Colonel Sumner fell out all those years ago, though the full story will be revealed in time. Again don't yell at me if some of the medical stuff was wrong, I'm just going off common sense and all that. Though next chapter has a bit more comedy from McKay that we all know and love, and bickering between our Mia and McKay, it's pretty comical if i do say so myself. Let me know what you all think, I love hearing your comments! See you next week!

Reply's

Adela - Well, we'll have to see whether she get's put into his team or not, shall we? ;)

Guest - Thank you so much! They won't always be in the background no, there will be a lot more interactions from this chapter on!

Guest 64 - Thank you, I don't like just giving up all my characters personality in one chapter, I like to spread it out so that they are more relatable. Of course there will be more John and Mia, originally I wasn't going to have them get together until Season 2 but I couldn't wait that long, so they will be together at some point in Season 1, but I'm not telling you ;) And thank you for saying that she's a good match for him, most John/Oc stories I read he always gets with a scientist, which isn't as exciting as he needs someone who can kick his ass from time to time.

parmakai66 - Thank you! Yes she is sassy, and she doesn't stop being sassy haha

Vadercat - I wouldn't call her an overachiever, more like she knows that she is kind of smart but she doesn't like to show it, unlike McKay. Truuuuuuuust me, there is a lot of bickering between the two later in the season about her intelligence about certain things.

Again thanks and don't forget to please leave me a little note!