A/N: I do not own SGA. Unfortunately. It's just one of the best shows ever.

Here's chapter 2, like I promised! Enjoy!

Chapter 2

A couple of weeks went by with the city being uncharacteristically calm and silent. The new members of the expedition had plenty of time to acquaint themselves with the new technology and their new home without the impending threat of the city blowing up, being attacked by alien species, virus' spreading havoc, you name it.

John walked into Elizabeth's office early one morning. "Does anything feel..off to you?"

Elizabeth looked up from her laptop and eyed the Colonel. "Not particularly. Why? Are you itching to go find us another problem to solve?" Sheppard starting pacing the floor in her office.

"It's just that my spidey senses are tingling. I don't know..maybe it's just because everything's been so..boring lately.."

There was a beat before Dr. Weir picked up on his hesitation. "But..?"

He stopped pacing and looked at her. "Something doesn't feel right." She closed her laptop and clasped her hands together on her desk. "I don't know, John. Maybe we finally just caught a break for once. Why don't you take the rest of the day off. Relax, spend time with your team. Maybe get to know some of the new people a little more. You never know, maybe it's just that you're getting anxious from having so much downtime."

John stopped and thought about what she was saying. "Maybe you're right. But if my spidey senses are tingling for a reason, you owe me a beer." She smiled and nodded. "You have a deal. Now go relax."

John made his way to the door. "Yes, ma'am."

He made his way to the mess hall to join his teammates for breakfast. When he arrived, the first thing he saw was Lt. Gordon marching over to where Nikki Teagan sat with some of her colleagues. He spun her chair around, grabbed her head between his hands and planted his mouth on hers. Immediately she started struggling against him, but he held her to him.

John ran over to them and grabbed Lt. Gordon by the shoulders. "That's enough, Lt.!" As soon as Sheppard's hands touched him, he snapped. Gordon let go of Nikki and then spun around so fast it was almost inhuman. He punched John across the jaw and sent him sprawling on the ground as if he were in basic training and not the CMO of an alien base. Gordon straddled John before he could move and starting punching the hell out of him. His strikes were so fast there was no way Sheppard could block him. Several marines tried prying him off of the Colonel, but he was too strong.

Ronon burst from his seat, crossed the mess hall in seconds and tackled Gordon to the ground. Vaguely he heard someone radio for a med team, but that was the last thing he heard before everything went dark.

About 4 hours later, John woke up in the infirmary with a nasty headache. He opened his eyes and looked around. Beckett was standing across the room talking to Rodney, Ronon, and Elizabeth. He looked to the other side of the room and saw Teyla talking to Nikki and Alex Teagan.

He tried to sit up, but a sharp pain split through his skull and he squeezed his eyes shut. He tried to stop a soft moan from escaping his lips, but he failed. In seconds Dr. Beckett was standing over him with Elizabeth right behind him.

"How do you feel, Colonel?" He opened his eyes and made contact with Beckett.

"Like I was punched with inhuman strength and then pummeled like a first year. What the hell got into him?"
"That's what we're still trying to figure out. There's nothing out of the ordinary about his scans, but we're keeping him isolated until further notice."

Now it was Elizabeth's turn to speak. "John, what exactly happened?" He finally managed to sit up with a little help from Carson. He looked around to see that Teyla, Nikki, Alex, Rodney, and Ronon had also joined the conversation. "Well, I went to the mess hall right after leaving your office. When I walked in, I saw Gordon walk over to Teagan, spin her around and kiss her. I figured it was just a happy greeting. Until she started to struggle. And then I remembered the little discussion I had to have with the Lt. the first day he got here."

Rodney interrupted before he could continue, "Was that about the fight in the mess hall?" John nodded and continued, "I told him that's enough and grabbed his shoulder to move him away from her. As soon as I touched him..it was like he just snapped. He spun around so fast I didn't realize what was happening until I was laying on the ground with a sore jaw. Before I could move he straddled me and was beating the hell out of me. I've never seen anyone move that fast. Last thing I heard was someone calling for a medic." He turned and looked at Elizabeth. "Oh, and you owe me a beer."

She sighed and nodded her head. "Yes, I do. From now on I'll trust your spidey senses." John smirked at her. "Good."

"Whoah, wait a minute now. Spidey senses? Is there something I should know here?" "Calm down, Doc. I just had a feeling in my gut this morning that something was about to happen. I went and told Elizabeth here about it, but she told me it was probably just the boredom talking and sent me on my way. And then as soon as I got to the mess hall, the suspicion was confirmed."

Ronon looked back and forth between Elizabeth and Sheppard. "Wait, so you knew something was going to happen.." He turned and looked at Elizabeth, "And you played it off as nothing?"

She blushed slightly and nodded. "And that was obviously a mistake. But, how about we divert our efforts into trying to figure out with the Lt. all of a sudden felt the urge to sexually assault someone and then pounce the Colonel."

"I agree with Dr. Weir. There has to be some explanation for why Lt. Gordon suddenly attacked by Dr. Teagan and the Colonel."

"Aye, Teyla, you're right, but nothing's coming up in the tests I've run. Rodney, have you checked the database for something like this?"

Rodney looked up from his data pad. "Actually, that's what I'm doing right now. So far nothing, but it's only one case, so therefore there's only a limited amount of data I can use to search for. There's a good chance it might happen again or has happened and we just don't know about it yet."

As if on cue, Major Lorne walked in supporting the weight of Dr. Zalenka. "Doc! We could use some help over here!"

Beckett rushed over to them. Lorne had a cut on his temple with blood dripping down his face, but otherwise looked fine. Radek was only partially conscious and was suffering from an even greater head wound and a gash on his thigh.

"Oh mercy! What happened?"

Ronon rushed over and helped the major with Zalenka. They carried him over to a bed and laid him down. "Radek and I were talking about some idea he had about an improvement to the jumpers. He barely started talking about it before one of the scientists went crazy. She started throwing things: computers, chairs, trays, you name it. I tried dodging to get to her to try to calm her down, but she got me with some kind of tool. She shoved me against the wall before I knew what was happening and tried running out of the lab. She threw Zalenka into the wall across the room and he crashed down on a table."

Ronon turned his attention on Lorne, "Literally threw him into the wall?" Lorne looked up at the big guy and replied, "Yeah, picked him up and just hurled him across the room as if he didn't weigh a thing."

Sheppard looked up at Rodney. "Well, there you go, Rodney. There's another case of inhuman strength with a dose of insane."

McKay nodded and started typing furiously on his data pad. Lorne looked over at the Colonel as if just noticing he were there. "Colonel! What happened to you?"

John turned and looked at his second in command. "You haven't heard the whole city talking about it?"

Lorne moved closer to the bed. "No, sir. Dr. Zalenka and I took a trip over to the main land for a while so he could run some test on something. We've been gone since 0700, sir. When did this happen?"

John looked down at his watch, "Oh, I'd say about 0730. Gordon attacked Nikki in the mess hall, so I stepped in. Damn Gordon knocked me to the ground before I could say yahtzee. Straddled my legs and knocked me senseless for a few hours."

Evan's brow furrowed. "So, what? Are we dealing with some kind of epidemic? That can't be a coincidence." Elizabeth crossed her arms. "No. It can't. Let's get to the bottom of this before more people get seriously hurt."

Alex spoke up for the first time during the entire conversation, "Major, who was it that attacked you?" "It was Dr. Lisa Cavanaugh. She took off from the lab. There was no way I could catch up to her."

Sheppard nodded and looked over at a nurse. "Can I go? I just got knocked around a little. I'm fine." She walked over and checked his vitals and then the stitches on the side of his face. She looked over at Beckett and saw that he was busy with Radek. "Your vitals are fine. I'm going to give you some aspirin for the headache. Come back if it gets worse or persists, got it?"

He nodded and swung his legs over the side of the bed. He stood up and swayed a little. Thankfully the only ones who noticed him sway were Lorne and Nikki. Lorne put a hand on the Colonel's arm to brace him. Sheppard nodded righted himself.

"Okay, let's get to the bottom of this before I start going crazy myself."

They all left the infirmary, minus Lorne, leaving Beckett to his patients. Walking down the hallway, John turned to Rodney. "Have you found anything yet?"

Rodney glanced up, "What are you crazy? I've barely had five minutes to search with the new information from Lorne. Give me a few minutes."

"Rodney. Lorne, Radek, and I got lucky. The next person may not be. We need to find out what the hell is going on with here and figure out a way to stop it." He turned to Elizabeth, "Elizabeth, I suggest we suspend gate travel until all of this is resolved. We don't want to spread whatever this is across the galaxy."

"Agreed. I'll go make the order myself."

Right before she left the group to head to the control room, John grabbed her arm. "You're not going anywhere alone. Not until this is over. Nikki, you can kick some ass. Go with her."

"Yes, Colonel." He turned and looked at her. She had a smug look on her face and winked at him as her and Dr. Weir walked down a separate corridor on their way to the control room.

He shook his head and turned to look at Alex. "I want you to go around and try to keep people calm. They're probably going to panic soon and that'll just make things worse."

Alex nodded and made his way to the transporter that would take him to the mess hall. Perfect place to start.

Sheppard and his team made their way to Rodney's lab. They didn't come across anyone who had suddenly gotten any violent urges, which was a good thing. But who knew how this thing spread, what it was doing to their people, or how to stop it.

They got to the lab and Rodney set up more laptops. He started reconfiguring the sensors that way they would be alerted when a major outburst happened.

Sheppard turned to Ronon, "We need to get to the weapon's room. Get some stunners so we don't have to use bullets on our own people." "Agreed."

Teyla walked up to John. "I will stay here with Rodney in case anyone should try to attack him while he is working. I will contact you in case we're alerted to an outburst."

Sheppard nodded and moved towards the door. "Sounds like a plan. Keep in touch."

Him and Ronon exited the lab and made their way to the weapon's room. Still everything was quiet. And then a woman was thrown over a railing and landed an entire story beneath. Sheppard rushed down the stairs and searched for a pulse. Ronon pulled out his gun and tried to target the woman who had thrown the other woman over the railing. She was already at the other end of the corridor and gaining speed. He fired once and it hit her between the shoulders.

It didn't even seem to faze her. He fired two more times before she finally went down with a tumble of her own. Sheppard appeared at Ronon's side. He looked down and asked about the woman who had fallen. Sheppard simply shook his head and made his way towards the woman Ronon had stunned.

She was laying there unconscious, but otherwise unharmed. "Medical team to levels 24 and 25."

He stepped over her and walked into the weapon's room. He grabbed a stunner for himself, one for Ronon and one for Teyla.

They made their way back to the science lab and he handed Teyla the stunner. "Any other outburst besides the one we took care of?"

She turned and looked at the screen. "Not that I've seen. What is the plan now?"

John seemed to contemplate the options for a moment before answering. "Ronon and I will head up to the control room. Any outbursts or any progress, let me know." She nodded and went back to monitoring the cities sensors for any signs of sudden outbursts.

Once in the control room, John and Ronon found people unconscious, but alive scattered among the floor. It was clear there had been a fight. He reached up and tapped his com. "Elizabeth, this is Sheppard. Please respond…Elizabeth, this is Sheppard. Please respond…Dr. Nikki Teagan, please respond. Nikki Teagan, I repeat. Please respond this is Colonel Sheppard."

He turned and looked at Ronon. "Nothing." "What do we do now, Sheppard?"

John looked around at everyone laying on the floor. "Medical team to the control room. Several wounded." He turned back to Ronon. "You check and make sure they're alive. I'll check communications just in case."

He picked up one of the laptops that had been knocked to the ground. Surprisingly it was still intact. He pulled up communications and found out that they had been manually disabled. There was no way for him to contact anyone on base. "New plan. Let's head back to the weapon's room and get radios. We'll distribute them to Rodney, Teyla, Lorne, Stackhouse, and anyone else we may need to contact. We'll set up a base in the mess hall. That's where Alex was heading when we separated."

They distributed the radios they collected to the infirmary, Lorne, Markham, Teyla, and Rodney.

"Sheppard! I know what it is." John clicked on his radio. "Good! What is it?"

"It's some kind of chemical that messes with the chemicals in the brain. That's why people are turning violent. This thing spreads through touch, so chances are we all have it by now. The database says it only works on those who don't possess the ancient gene. Well, that's a relief. At least the entire base isn't about to go nuts."

"No, but most of it is and those aren't good odds. Is there a cure or antidote? Anything to stop this?"

There was a long pause of silence. "Rodney!" "Yes, hang on! I'm still trying to figure that one out. I'm going to send this information to Beckett. Maybe he can figure something out."

"Good idea. We're heading to the mess hall to set up a control center. Meet us there."

"Understood. McKay out."

Ronon glanced over at Sheppard. "Well, at least we know what it is now." "Well aren't you ever the optimist." Ronon grunted and continued walking towards the mess hall.

Once the control center was established and several people were relocated to the mess hall for refuge, they started to formulate a plan. Elizabeth and Nikki walked right as they were working through their options.

John looked up and saw Weir's panicked expression and Nikki's more calm and in control expression. He took a wild guess and assumed they had been attacked or very nearly on their way here.

A good portion of the base made it to the mess hall. About one fourth of the expedition had fallen "ill" due to the chemical and they were running out of options and out of time.

"Colonel! Do we know what this thing is yet?" "Where the hell have you two been? And yes, we do. We're working out a plan now."

Nikki stepped up beside John. "When we got to the control room, it was under attack. I didn't want to take the risk of Dr. Weir getting hurt so we snuck out undetected and hid in the jumper bay for a while, waiting for the control room to empty. And then I figured you'd set up a control center here and we've been trying to make our way here ever since."

John nodded and turned back to the group. "Okay. What are our options?"

Rodney looked up from his pad, "Well, we could set the self-destruct and abandon the city. You know..as a last option." Weir stepped into the group. "That's not an option. What else?"

There was silence. And then Nikki spoke up. "Has Dr. Beckett or McKay found any sort or antidote for it?"

McKay looked back up from his pad. "No, I have not. I have been looking, but there's nothing here. I think we're on our way on this one, Colonel."

John nodded and looked around at everyone. He pressed the button on his radio, "Beckett, this is Sheppard, come in." "This is Beckett."

"Doc, have you come up with anything we could use against this thing?"

There was a moment's pause and then, "Aye, I have, but you're not gonna like it."

Half an hour later, Sheppard, Ronon, Teyla, Rodney and Nikki were all standing in the infirmary standing around Carson's lab table. "Okay, Doc. Let's hear it."

Beckett looked up at the Colonel. "Rodney was wrong. There was something in the database. He just looked right over it. I would have too if I hadn't have been looking back over it a dozen times since I first got it. All we have to do is release a certain chemical into the air. That chemical will counteract the effects of the chemical that is now effecting them."

"Okay, get to the part that I'm not going to like."

"It has to be administered by those with the ancient gene. Otherwise the effects of that chemical will cause serious side effects."

Rodney about jumped for joy. "That's it? That's all we have to do?"

"Sadly, no. Since not everyone who doesn't have the gene has been infected by this damned chemical, we can't simply put it through the air vents. That would be disastrous. The only other way is to inject each person infected by it when the chemical from a syringe. And that's where the tricky part comes in. You'll have to get close enough to them to inject them."

Ronon put his hand up, "Wait, why do we have to have the ancient gene in order to inject with a needle?"

"The new chemical omits a type of pheromone, even in liquid state. For anyone who does not possess the ancient gene to come into contact with that pheromone would be bad. Very bad."

John was getting tired of this. "Okay. That means Elizabeth, Teyla, and Ronon, you're sitting this one out. Rodney, better get over your fear of needles fast and learn how to use them. Nikki, do you have the gene?"

She looked up at the Colonel and saw hope in his eyes. "Yeah, and from what I hear, I have a pretty strong dose of the stuff too."

"Aye, hers is almost as strong as yours, Colonel. The three of you will have to be fast and make sure all of the chemical gets into their system."

They spent the next fifteen minutes being given a lesson in Needles and Injections 101.

Teyla and Ronon took Elizabeth back to the mess hall, just to be on the safe side. John, Rodney, and Nikki got geared up and set up a way to convert the life signs detectors from the jumpers into sensors that would tell them if someone was infected by the chemical.

Once they got the detectors and then configured them properly, they split up. There were at least thirty people they had to inject with the new chemical. They each got ten a person. Before they went their separate ways, Sheppard turned and looked at the two. "Every time you inject one, radio it in. Understood? That way we can keep tabs on how many are left. And make sure your position is known to this group so there aren't any more problems."

They nodded their heads and split up. Five minutes into the searching, Nikki's voice came over the radio, "Got my first one and am coming up behind the second."

John pressed his radio, "Copy that. I'm about to get my first. Rodney?"

There was silence for a moment. "Yeah, just got my first. I hope."

"You hope? Did you get 'em or not?"

More silence.. "Yeah, I got 'em. Moving onto the second."

Soon they had injected twenty-five out of the thirty people. They had only run into few problems so far.

And then the one John was after snuck up behind him, shoved him against the wall and tried biting his neck. He braced one arm against the woman holding him, keeping her a little distance away from him. He barely managed to reach around and grab the next injection and stick it into the side of her neck before she knocked his arm loose and actually bit him. He screamed out in pain at the same time she did from his stabbing her with the needle.

He pushed her back and she collapsed on the ground. He reached up for his radio. "Well..another one bites the dust. And took a chunk out of my neck. I think they're getting territorial. Watch your six."

Rodney radioed in, but John had yet to hear from Teagan. She wasn't responding to her radio. "Rodney, can you locate her?" "Hang on, let me check."

A minute goes by and then the radio clicks. "Yeah, she's..about two levels below you with..oh god. There's two of them in the same room as her. You better get down there, Sheppard!" Rodney hadn't even finished his sentence and John was already running full steam down the levels toward her.

He stopped outside one of the rooms on that level when he heard scuffling. He peered in and saw Nikki gab the needle in her hand into the side of the man's neck who was standing in front of her. There was also another man sneaking up behind her.

The man lurched for Nikki, knocking into her and sandwiching her between the man she just injected and the man that attacked her. John lunged forward. The man was clawing at her back, trying to tear her apart it seemed. She was too big for him, one of the more experienced marines.

Right before the man snapped her neck, John jammed the needle into his neck and he went limp almost instantly.

He looked up at Nikki who just stood there speechless. "Are you okay?" She nodded and looked down at the man lying on the floor. "Thanks. He almost killed me." "No problem."

She looked up and saw the blood running down the Colonel's neck from where the woman had bit him. She moved towards him and grabbed one of the compressant bandages from her tact vest. "Here, hold still. You're bleeding." "I am?"

He reached up to his neck, and sure enough there was blood. He stood there as she pressed the bandage to his neck and then wrapped it around his neck and fastened it to keep it on. "There. That should do until we're done." "Now it's my turn to thank you." She smiled up at him and nodded. "Why yes, yes it is." He smiled and they just stood there for a few moments just staring at each other smiling.

And then Rodney's voice came over the radio, making both of them jump, "Sheppard? Nikki? Hello!"

John reached down and clicked his radio. "We're fine, McKay. We got both of them. Two left. We'll go after the one closest to us. You got the last one?"

McKay snorted. "Yeah. Sure. Why not. Let's just get this over with so I can take a nice long nap." John rolled his eyes and looked down at his sensor. The other one was one level down.

They made their way down there quickly and quietly. Nikki went for one side while he went for the other. She accidentally stepped on something and it broke, making a loud, echoing noise in the room. The woman stopped and turned in her direction. Then slowly moved towards her location. John jumped out from behind the crates he was hiding behind and stabbed the needle into her neck. Right as she dropped to the floor, Rodney radioed them saying he was done.

They made it back to the infirmary and told Beckett where all the people had dropped so his med teams could go find them. He waved off Carson's inquiries about his neck and quickly left the infirmary when he was distracted with something. He made his way to the mess hall and informed everyone it was safe and that the threat had been eliminated.

Mass cheering went up in the mess hall and he sank down into a chair, exhausted. Nikki joined him and soon the rest of the team did as well. Elizabeth walked over to their group. "Nice work, John."

He looked up at her. "Thanks. So, Elizabeth. When do I get that beer?"

Okay. So, what did you think? You can probably tell how tired I was when I wrote this..I really wanted to get it finished before I went to bed. I did my best..sorry if I left things out or if it was confusing. I need ideas about later chapters, please! Review! =)