Disclaimer: I do not own Stargate Atlantis and no infringement was intended, just having some fun with the characters.
Spoiler Alert: Major spoilers for "The Seed", and minor ones for previous episodes, especially "Search and Rescue"
Summary: Some of John's thoughts in "The Seed" and a few extended/missing scenes.
A/N: Baileysmom commented that these aren't really tags, but are more like synopsizes of the episodes…to which I say…uh…yeah…it…a…sort of is…(clears throat) However, the reason it is that way is I am still getting used to writing stories directly about the episodes, instead of coming up with my own completely separate plots. I should get better in time, and make them less of a repeat of the episode…hopefully anyway…Enough about that, however, and here is my…missing scene/synopsis thingy for The Seed…
The Seed: A Bad Few Days
Sheppard groaned as he felt the pain flair up in his side again. It had been a really bad few days. The day it had all begun had started out okay enough, but it soon spiraled out of control in a downward loop that landed at his present miserable condition.
He had awoken at his normal time and gone on a walk/jog with Ronon. Dr. Keller had absolutely forbidden running as he was not fully healed from having a building collapse on him, but she had tentatively agreed to the walking and jogging as long as he didn't overdo it and did more walking than jogging.
Sheppard tried to explain to her that he was perfectly fine, and he needed to build his stamina back up from having laid on his back for an entire week, but she just looked at him with a look that clearly said, 'you still owe me from letting you rescue Teyla, don't even think of trying to push your body right now.'
So sighing he had been taking it easy…well easier...okay at least he wasn't outright running, which was the main goal…right?
Ronon and John had then met up with Teyla and Rodney for breakfast in the mess hall. Teyla was holding Torren and looked tired, but content as she gazed at her son.
"How's the little guy doing?" questioned John as he set a tray before Teyla and then placed his own at his spot.
"He's doing well, though he seems to think his mother doesn't need any sleep."
John grinned at Torren and said, "So he's already being a trouble maker, huh? And Rodney hasn't even taught him any of his tricks yet!"
"Hey!" was Rodney's indignant reply, while Teyla looked at each of them in turn and said, "I'm not sure I want to know what each of you will be teaching him."
Ronon and John simply grinned at each other as they thought of all the fun they would have with Torren once he was older.
However, Rodney interrupted his pleasant thoughts and began the spiral that ended with John on his knees with a vine like thing sticking into his side.
"Isn't this the day Woolsey is coming?" And in a moment all John's ideas of having a nice day were shot.
Groaning he remembered his first encounter with Woolsey. Woolsey had been reviewing Elizabeth, and John had found that it took all of his strength to not beat the guy to a bloody pulp, and now here he was coming to lead the Atlantis expedition.
John couldn't think of someone less qualified to lead the mission, though he supposed the city would be completely caught up on paperwork with in a week, which reminded him, "Shoot! I still have to write up a report on an incident from yesterday!"
"Well, at least that is all you have to do," moaned Rodney. "I haven't done any of my reports for the last week, and I just know he's going to want them."
John nodded, if it was one thing they knew about Woolsey, it would be that everything would need to be done by the book, including getting all paperwork in on time.
Sighing he got up from the table saying, "I need to get that taken care of and make sure everything is up to inspection in the military contingent before he shows up today. I'll see all of you later." He nodded to each of them, and grinned at Torren who had his eyes open.
Tearing himself away, John made his way to his office and made sure there was nothing that Woolsey could complain about in his neck of the woods.
Hours later after he had examined every possible thing Woolsey would be looking at, he made his way to the control room knowing that Woolsey was due to arrive. A technician informed him that the Daedalus had dropped out of hyperspace, and that Woolsey would be being beamed down shortly.
He tried to keep his lack of…excitement…at Woolsey's arrival under wraps as he stood ready to meet the new leader of the expedition.
When Woolsey arrived, he was exactly as John had remembered him, down to the briefcase held smartly in his left hand. Seriously…who brought a brief case to another galaxy? Shaking off these thoughts John made his way to Woolsey.
After the initial greeting, John watched as Woolsey began to speak. John remembered the speeches of both the previous Atlantis expedition leaders as they took command, and wondered what Woolsey would say.
Though he wasn't exactly sure what he expected, Woolsey's 'speech' had definitely left something to desire.
His speech had consisted of "Well then…" followed by a long pause and then in a more normal voice, "I think I'll start by going over copies of all your latest reports."
John's eyes had widened as he took in Woolsey's speech and he felt his apprehension grow at the idea of this man being the new leader of Atlantis.
He heard Rodney's voice asking "What, right now?" and realized the astrophysicist must not be fully caught up on his reports.
After Woolsey left, John commented to those nearby, "Nice speech, very inspiring."
John then spent the rest of the day helping Rodney get caught up on his reports, which was one of John's least favorite things to do. He disliked doing his own paperwork enough that the idea of helping with someone else's was less than thrilling.
The next day had started in the same way as the previous one, but with the ominous first briefing with Woolsey hanging over his head. By the time he reached the briefing, his team and Keller were already there.
He grabbed a cup of coffee as they talked about Woolsey taking over for Carter to help keep him fully awake and focused throughout the meeting.
When the topic of conversation shifted to what he had learned of the alternate future and how Woolsey had taken over in that timeline too, John quickly glanced over at Teyla reminding himself that all the horror that had occurred in that timeline was not occurring in his.
As Rodney tried to reassure himself and everyone else that Sheppard being here on Atlantis now was enough to fix everything, John, thinking of Rodney and Keller together, said, "Woolsey wasn't the weirdest thing about that timeline."
"What do you mean?" questioned Keller as John thought again of how surprised he had been that Rodney and Keller had fallen in love.
With a strange look on his face, realizing there was no way, he was going to be telling anyone about that relationship he said, "never mind" right before Woolsey entered the room.
The following briefing had been a practice in John's self control as he clamped down his growing frustration with Woolsey as Woolsey explained that he would not devote any resources to looking for Michael, despite the hundreds of thousands Michael had killed, and that he would not be releasing the prisoner hybrids any time soon. Then he had pressured Keller into doing the procedure on Carson, though she was unsure if it was ready.
After the insufferably long meeting, John had been called away by Lorne to deal with some new marines, so he had been absent when they took Carson out of stasis. However, he had managed to be present when Carson awoke again in the infirmary. He had watched with concern as Carson opened his eyes slowly and asked what happened.
When he told Carson that he had been in stasis for about two months, John realized that he no longer felt that two months in stasis was that horrible. After seven hundred years how could he?
Then Carson had asked if he had missed anything in that time. John's mind quickly flashed to all the things that had occurred, from his traveling 48,000 years into the future to Michael's booby trapped building and Teyla's rescue.
"You know just the usual."
Keller soon entered the room and John was filled with concern for her. She had been working none stop the last few days…well weeks actually. First, on getting everyone, including himself, fixed up from the explosion of Michael's building. Then she had worked on a treatment to get all of Michael's hybrids back to normal, while simultaneously finding a cure for Carson. John knew she had not been getting much rest lately, so as she went to leave the room, he stopped her.
He could tell from their brief conversation, she was already trying to think of a more permanent solution to heal Carson, but he needed her to get some sleep. She was rundown, and he knew from all the lecturing he himself always seemed to receive that you were no good to anyone, if you didn't give yourself a chance to recuperate.
So, he straight up told her to get some rest. She quickly agreed for which he was thankful, and as he watched her walk away he was filled with worry that the strain of the last few weeks was getting to her.
The next day he got the news from Woolsey that he was sending Carson back to earth. Though, John had contained his frustration, it was difficult to think of losing Carson again, after only just getting him back. The fact it clearly hurt Rodney deeply didn't help matters either, and John found himself making his way to the gym to beat the crap out of a punching bag.
John wasn't sure if Keller would approve of his choice of methods to take out his frustrations, but he was mad enough, he really didn't care. John hated how Rodney looked as if he was about to lose his best friend again.
After hitting the punching bag until his side gave off more than a vague ache of pain, he had calmed down some and taken his second shower of the day. He had just been talking with some of the marines when he got a call over his radio.
"Colonel Sheppard this is Teyla."
She sounded worried, so he had immediately answered, "Go ahead."
"John, we have a problem."
He raced over to Keller's room with the marines he had been talking to and found to his horror all sorts of vine like things attached to Keller. Careful to not touch anything, John had crouched by Keller's bed and taken in her stillness.
Carson's explanation of where he had seen something like this before did nothing to relieve John's growing panic and fear at what was happening to Keller. Imagining how horrible it would be to have those things connected to him, he said, "Well, we've got to get it off her!"
John felt the panic continue to rise as he heard Carson's reasoning for why they couldn't do just that.
Frustrated he said, "Well, we can't just leave her like this!"
Carson explained that they needed to take her and the bed to the isolation room to examine her and John found himself desperately hoping that Carson's skills as a doctor would be enough to get rid of whatever was growing out of Keller's body. He swallowed as everything around him continued to spiral downwards.
After Keller was set up in the infirmary, John had the unenviable position of updating the new head of Atlantis. He explained what was happening and then had to deal with Woolsey's by the book philosophy. John explained that no one knew more about the thing attached to Keller than Carson, and hoped that Woolsey could ignore the book for a bit until this 'problem' as Teyla called it got taken care of.
Luckily, Woolsey did at least for the moment. John watched with the rest of his team and Woolsey as a host of medical personnel worked with Carson around Keller. He felt his fear escalate as he heard someone say, "She's crashing!"
When the heart monitor evened out and Carson said, "there she is", John realized that he had been holding his breath and let it out. As Carson explained that that avenue was not going to work, John looked intently at Keller as Ronon voiced his own thoughts, "So much for cutting her loose."
This day was really sucking.
Woolsey took Carson aside to talk with him and John hoped he wasn't sending him back to earth just yet. When Carson returned to work, John commented, "You're not sending him back, huh?"
Woolsey responded by reflecting what John had told him earlier. "Well, he is the closest thing to an expert we have."
Wanting to make sure Woolsey knew what he was doing, John said, "It's not exactly by the book."
"Don't get used to it."
John nodded, he didn't expect to. Then he turned his eyes back to Keller who was lying perfectly still on her bed.
Late that night John discovered there was some weird alien pathogen in Keller's blood stream and Carson wanted everyone who had been on the planet with Michael's lab to have their blood tested for it. John hated having his blood drawn, and hated even more the idea that there was an alien pathogen in his body.
Early the next morning he got the news; not only was he infected, he also was being quarantined in his room. When Woolsey came to talk to him, John was ready with his list of reasons for why he shouldn't be quarantined.
"We've been back for a month now! If it was gonna spread to the general population, it would have already happened."
"I know. Doctor Beckett is now fairly confident that it's not contagious."
"Right. Then why confine us to our quarters?"
Woolsey's long speech that followed did nothing to relieve the frustration and anger Sheppard was feeling. In fact, it made it worse. Woolsey explained that though Sheppard might not have experienced any changes yet, he definitely might start soon. There was a way to make the last couple of days Sheppard had been having even worse. Tell him everything he saw going on with Keller was going to happen to him!
Sheppard hated being confined to quarters, hated not being able to protect the people on this base, hated not being able to help Keller. He pretty much just hated this entire situation.
However, Woolsey's last comment about it being the right call, he couldn't totally disagree with, not that he didn't disagree, because he really did, but he understood where Woolsey was coming from.
Worry over Keller made John catch up to Woolsey before he left the room. "In the meantime, what are we gonna do about Keller?"
John felt his stomach clench as Woolsey simply said they were still assessing the situation. When the door shut behind Woolsey, John felt like his life was spinning out of control.
The next hours spent alone in his room were slowly driving him crazy. Finally, Teyla stopped by his room to update him. The information was far from encouraging, and he hated the fact Keller had been left alone in the isolation room. Teyla soon left to update Rodney as John knew Rodney was probably feeling even crazier than John was locked up and out of the loop.
When he discovered that Teyla and Zelenka were going to be doing recon on the hive ship growing on Atlantis, John hoped that nothing would happen. John wished he was on the mission and making sure everyone was doing okay, but he knew that he had to be patient for their return.
The news they brought back, left much to be desired. The fact Zelenka got a concussion made Sheppard want to grind his teeth with frustration. He should have been there to make sure everything went okay.
Sheppard's silent ongoing rant was interrupted by a radio call. Woolsey wanted to meet with him, Rodney, and Ronon in John's room. During Woolsey's update, John knew exactly what Woolsey was doing. Without right out asking, which John would have preferred, Woolsey was trying to get John to agree to test the unknown treatment on him. John knew from the beginning he would do it, though he was slightly irritated that Woolsey wouldn't just ask him, so he didn't agree to do it until Ronon offered to have the unknown substance tested on him.
"No, no, no, no" he told everyone and then looking straight at Woolsey to let him know he had known from the beginning what he was doing he said, "I'll do it".
As John was put in restraints, he almost wished he hadn't agreed to it. Restraints always reminded him of various times he had been tortured, and he always felt his heart rate quicken because of them. Carson's following talk, did little to settle that heartbeat.
Everything he said made Sheppard feel worse. First, "I'm anticipating a severe reaction", then "the formula comes from Michael's lab", which made John instantly think of being turned into a bug. Another thing, he wasn't exactly fond of. Finally, Carson said, "Actually, "it could kill you."
John felt his frustration rise and he just wanted to have the damn shot before he had enough time to think about how absolutely horrendous this idea was.
There was a small amount of pain when it was first injected and then John, who based on the words "severe reaction" had expected something immediately to happen, was surprised that he didn't feel any different.
When Carson then told him just to relax while he waited the few minutes for it to kick in, John couldn't believe his ears.
Sure he'd relax as some untested drug was just put in his system to which he would probably have a 'severe reaction', whatever that might mean, before he possibly died. Relax? Sure! it'd be a piece of cake.
Suddenly, while John was talking with Ronon he began to convulse. The pain was spreading from his head and neck, were the drug had been injected to the rest of his body. Trying to not let on just how much he was in pain, he said, "Oh, I think these restraints were a good idea."
The convulsions and the pain grew stronger and John tried to not cry out in agony, while everyone was watching him. As his body violently shook him around the bed, John tightly gripped the infirmary bed. Yet, soon he wasn't even aware of what was occurring around him. The pain was all consuming. It felt like a battle was going on in every part of his body, which in a way it was as the drug attacked the alien pathogen in his blood.
John felt hands on his shoulders and pushed through the tremendous pain that had seemed to go on for hours, and realized it was Ronon.
Then the pain and convulsions reached a crescendo, and though John tried to hang onto consciousness, he found that it was too much for his body and he blacked out.
John later discovered that his heart had stopped. Yeah, definitely a bad couple of days!
It didn't get much better after that. When he had fully awakened hours later, he discovered that Ronon was trying to give Keller the shot and it wasn't going well.
He began to formulate a backup plan and reached the control room shortly after Ronon no longer responded to any hails.
John had felt sickened when he heard the…thing…talking about Ronon, and how easy it was to kill him. Trying to do anything he could to keep Ronon alive, while he enacted his plan he said, "Yeah, but you don't wanna do that because he's—he's one of you, remember?"
In a moment John was on his way again, hoping that his plan would succeed. Shortly after powering up the jumper, Woolsey had hailed him. Unable to completely bite back his frustration he said, "I'm takin' a little shortcut. Sorry I didn't have time to fill out the paperwork."
Getting close to his destination, he realized that intentionally crashing a jumper into their own city was not the best idea, and couldn't help but say "This may hurt."
He braced for impact as he closed the drive pods and tightened his grip on the controls. Then he hit.
It was just as bad as he had imagined it would be. Sparks were flying everywhere burning his hands as he fought to maintain control of the jumper. Finally, the jumper slammed to a halt and John found his own body jar against the console.
For a moment, John was dazed. All he could process was the pain he was in. Apparently, crashing into the city hurt even more than he thought it would. Go figure.
Clearing his fuzzy thoughts, John remembered the danger to both Ronon and Keller and pushed himself to his feet. He needed to get this thing taken care of before the—baby hive ship—recovered from the trauma he had caused it.
He carefully made his way to the isolation room, thankful that the thing was definitely out of it still and was not attacking him. He quickly gave Keller the shot.
For a moment, nothing happened and he feared it hadn't worked. Then Keller gasped and the vines began to twist and curl. He looked around warily and then suddenly a vine attacked him. It pierced his side, and Sheppard gasped in pain.
He crumpled to his knees favoring his right side. He raised his gun and pointed it at Keller's head. He prayed that this had worked, but if this was the only way to stop the hive ship and protect Atlantis he would do it.
Then suddenly everything went still. He slowly lowered his gun thankful that he had not had to use it. The pain was tremendous a constant throbbing pain, that he was sadly all too familiar with. He pushed past the pain and heard Woolsey's voice over the radio. Finally he managed to respond and let him know he was still alive.
It was getting harder to talk and John pushed himself to weakly say, "You'd better come get us."
John looked down at the vine extended out of his side and swallowed bile as he realized just how thick it was. He stopped himself from shuddering at the idea of that thing being in him, he knew if he did that would cause excruciating pain. As it was, the pain was already agonizing. If the vine had attacked any other part of his body it probably wouldn't have been so bad. Yet, the vine had taken the information from Keller and had attacked the area that was still tender and healing from Michael's building falling on him.
It truly had been a bad few days, and now he had a stay in the infirmary to look forward to. Joy.
John leaned over to the side more, trying to decrease the pain that was overwhelming him. Every time he took a breath the pain increased making him want to just hold his breath, yet he felt like he wasn't getting enough air as it was, and it was only by force of will that he wasn't outright panting for breaths already.
Through the haze in John's mind he looked over at Keller. She was still staring up at the ceiling and he realized how horrifying this must be for her. Trying to reassure her he said, "Keller, it's going to be okay now." He paused to catch his breath and then doggedly continued as he noticed her frightened gaze had met his eyes. "Everything is fine…You're gonna be…back to normal…in no time."
By the time he was done with his little speech he found that he could barely breathe. He wanted to just curl up on the floor, but knew that with the vine still in his side that would be a monumentally bad idea. Much worse than his normal bad ideas, and he forced himself to remain kneeling.
He noticed his knee felt wet and watched in fascination as blood ran down his side to puddle around his knees.
"…Colonel?" a weak voice asked.
"He looked up and met Keller's eyes. They were still filled with confusion and fear, but they were also aware.
"…hey" he grunted. "…medical teams are…on their way…"
She nodded and John simply panted trying to recover the breath talking had cost him. He was finding it harder and harder to concentrate on anything as it felt like something was sticking out of his side…oh yeah…a vine was sticking out of his side.
He felt himself list to the side some more, and he couldn't hold in a small cry of agony as the movement caused the vine to shift inside of him. How long was it going to take everyone to get here anyways?
John tried to focus on anything but the pain, but discovered it was pretty hard to ignore something when you had been impaled you and the thing that impaled you was still in you.
Right when John felt as if he wasn't able to remain upright any longer he was aware of hands grabbing his upper shoulders to hold him steady. He blearily looked up and saw that the rescue team had arrived. He tried to focus on the doctor in front of him as she asked him how he was doing.
He wanted to say 'how do you think I'm doing?', but settled for grunting.
Hoping that Ronon was okay he weakly asked, "…Ronon?"
"He's alive and going to be fine. I need to cut the vine, and it will probably hurt, okay?"
John knew that hurt would be an understatement, but he nodded anyway. However, as soon as she began to cut the vine John realized that he preferred Ronon's simply yanking the pipe out of him to this slow methodical way of torture. Every slice made the vine shift slightly inside of him. Soon it became too much for him to bear and he slipped into darkness.
John awoke to a soft crying by his bed. Confused at first by what made the sound, he shifted his head and saw Teyla holding Torren John in her arms.
It looked like she was on her way out, so he said, "hey".
She stopped and turned back towards him. "John!" she said with a smile. "I'm sorry we woke you. Torren was asleep, so I thought it was safe for me to stop by and see you, since Keller said she was done with the surgery, but as soon as I stayed still too long, he awoke again."
"Don't worry about it. How is he?" John looked over at the tiny boy in Teyla's arms and couldn't help but smile at it. He carefully reached out his hand towards the still crying baby as Teyla brought him closer. He put his finger by the little tykes' hands and felt a thrill of wonder as Torren grabbed it and stopped crying momentarily.
John was always amazed at how tiny Torren's hands were when they grabbed his finger which suddenly felt massive and clumsy. He glanced up at Teyla's face and saw her smiling down at them.
Suddenly, Torren let out another wail, and Teyla sighed. "I must be on my way, but I will check on you again later, John."
"Okay," John smiled, however, his smile faded as he saw Woolsey approaching him. Had he mentioned how bad his last few days had been?
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The end of another episode, but there are plenty more episodes to go :D
A/N: I know this is sort of a repeat of the episode, but I love thinking about what John's thoughts would be throughout what is happening to him and I am still getting used to this tag thing :D. I will try to make the next episode I do less of the synopsis and more of the tag or missing scene…