Disclaimer: Unfortunately, I do not own Stargate or its characters; however, I enjoy writing about them.

Disclaimer: I am not a medical professional or a doctor. Although I try to research medical terms, they may not be 100 percent accurate.

This story takes place a few weeks after the events of 'The Shrine."

It's been a while since I last posted anything, but life has been busy, and I haven't had the time to create. I hope you enjoy it.

Chapter 1: The Ancient Lab

John Sheppard gazed around Rodney McKay's chaotic lab, his eyes mixed with amusement and bewilderment. The scientist's ability to navigate this organised chaos was a marvel. However, Rodney's lab wasn't always this chaotic, unless something bothered him, and John wondered what it was. Maybe he'd ask him about it, or perhaps he wouldn't. The last thing he felt like was an emotional conversation, and he was positive Rodney wouldn't want to talk either. Maybe it was a result of the parasite that had almost killed him a few weeks ago.

A string of numbers and equations adorned a whiteboard; had he bothered to decipher it, he might have understood Rodney's current project. But the intricacies of Rodney's mind always intrigued him. Despite their differences, they had shared countless adventures, from battling Wraith to exploring new worlds and even surviving the Pegasus Galaxy's most dangerous missions. Rodney's lab starkly contrasted with the man's complex intellect, which was why John suspected something was wrong.

The infirmary - where he'd spent the last twenty-four hours - was too quiet, and the absence of his team made the base feel empty. A game of chess or a lively debate might have provided some relief. Or they could have indulged in one of the newest DVDS the Daedalus had dropped off a week before, a collection of classic Earth movies that always managed to entertain them, anything to break the monotony. He'd even watch something of Rodney's choosing; he was so bored.

Jennifer had released him from the infirmary that morning with strict instructions to stay out of trouble, which he had every intention of doing—he never willingly got into trouble. It wasn't his fault his shoelaces were untied, and he fell down the stairs, breaking his right arm and hitting his head—how embarrassing. The stairs were slippery from a recent rain, and he didn't notice in his rush. So now his arm was in a cast to his elbow, and he had five stitches in his head, not to mention a headache. Luckily, he didn't have a concussion.

Teyla and Ronon were visiting the Athosians and had taken Torren with them. As usual, Woolsey was busy with mounds of paperwork. When John offered to help, Woolsey laughed at him and told him to go and enjoy himself because he was supposed to be on medical leave for the next few days—doing what he had no idea.

After the falling incident, he had to endure Rodney's laughter. However, when Rodney realised he was injured, he became serious. That was until Keller declared that his injuries were only minor. So he had no idea why he was seeking him out now. Knowing Rodney, he'd just mock him again.

Sighing, he turned to leave the lab and was startled when Rodney came rushing in, and he needed to grab the desk to stop from falling. Jennifer had assured him that there was nothing wrong with his coordination or balance after he'd fallen down the stairs. She'd declared it was an accident. That didn't make him feel any better because John Sheppard wasn't that clumsy. That was why John had asked her to perform several tests to check his coordination and balance.

"What are you doing here, Sheppard?" Rodney asked as he dumped his computer on the desk, entering the room without regard for his precious device.

John looked at him closely to see if he could detect anything wrong with his friend, and he shuddered; since when had he become so emotional? He assumed it was due to the Pegasus galaxy parasite that had almost killed Rodney recently.

"It's good to see you, McKay," he replied sarcastically, not wanting to worry needlessly about his friend.

"Well?" Rodney asked, but John didn't know whether he was ignoring or oblivious to the sarcasm.

"I'm bored. Do you want to do something?" John asked, his voice tinged with a hint of anticipation. He watched as Rodney's eyes lit up with excitement. The scientist clearly had an idea, and John stood, staring at his friend, waiting and hoping it would be fun.

"Do you feel like exploring an ancient lab I found in the deserted areas of the city? I'm not sure what the Ancients were doing there, but with your help, I'm sure we could find out."

John's eyes lit up with relief at Rodney's suggestion. An ancient lab in one of the city's uninhabited areas sounded like a fantastic idea. " Sure, let's go." The prospect of exploring the ancient lab was a welcome escape from the mundane routine of the last few days. However, he was positive that they could both end up in deep trouble, but that was nothing new, so he wouldn't let anything stop him.

John headed for the door, but Rodney remained rooted to the spot. " Are you coming because I'm fairly sure I don't know where this ancient lab is?"

"Are you sure you're okay, Sheppard? I'm happy to wait another day or two if you're not up to it." Rodney suggested in an uncharacteristic display of kindness.

Great, now Rodney wants to get emotional. John thought before putting on a fake smile.

"I'm fine, Rodney," he lied. His head was pounding, and his arm was aching, but he wasn't going to tell Rodney that because he needed to do something to relieve his boredom. Besides, he'd taken a couple of Tylenol before entering Rodney's lab, so he hoped it would kick in soon. He was determined not to let his physical discomfort hinder their adventure.

Rodney stared at John, making him feel increasingly uncomfortable. Ultimately, the scientist nodded and walked past him to exit the lab, relieving John from the awkward scrutiny.

Five minutes and two transporters later, they were walking through the deserted areas of the city, and the first thing John noticed was the smell. It was probably due to the mould growing on the walls, a testament to the storm damage they'd suffered from the vast storm the first year on Atlantis. Although the shield had protected most of the city from the storm, water had managed to get into the lower levels. However, the city had clearly suffered water damage in these areas long before that storm. The dark and damp tunnel made John shiver - and it wasn't due to the cold. Who knew what was lurking in the depths of Atlantis?

Rodney's loud complaining brought him out of his contemplation. " What is that smell?" the scientist asked, putting his arm over his nose.

"It has something to do with the mould growing on the walls, or something has died in here," John commented with humour, turning on his flashlight to give them extra light. John was careful not to slip as they continued down the dark, damp corridor; the last thing he needed was to end up in the infirmary from another stupid accident.

They passed by a window and were surprised to find themselves underwater, looking out at the ocean. The sight of the water on the other side of the glass, the gentle sway of the seaweed, the aquatic life, and the muted light filtering through the waves piqued John's curiosity. He couldn't help but wonder if a leak was responsible for the corridor's wet and slimy condition. If it were, would the glass crack and break, causing water to rush in and drown them? John shuddered again at his disturbing thought.

Sensing John's unease, Rodney reassured him, "Don't worry, Sheppard; I'm pretty sure the windows are thick enough to keep the ocean out. It's held back the ocean for ten thousand years after all.

He nodded, but his self-chastisement was loud in his mind. How could he have been so stupid? Of course, the window would keep out the ocean - at least, he hoped it would.

They continued their journey in silence, the path becoming less slimy and cold. John soon realised they were walking uphill, and he couldn't help but wonder if there was another, less challenging route to the lab Rodney was so eager to reach.

"How much longer until we reach this lab of yours?" John asked, beginning to lose patience.

"Since when have you been so impatient, Sheppard? Usually, I'm the impatient one. We've only been walking for half an hour."

"Yeah, sorry," he muttered more to himself than to Rodney. He had no idea why he felt so antsy. Maybe it was the unfamiliar environment or the constant dread that something could go wrong at any moment, but that was just another day at the office for him, so why should he be worried? He shook his head, trying to dispel the unease in his gut.

John followed Rodney for another few minutes before the scientist stopped." I think we're here," Rodney commented, stopping beside a closed door.

For the first time since he'd left Rodney's lab, John's mind was filled with concern about the Ancients' research. He wondered if Rodney knew what the Ancients were doing in this lab. "Do you have any idea what the ancients were doing here?"

"I think they were researching the possibility of Alternate realities." Rodney surmised.

John's face darkened at the news. The memory of their narrow escape from the experimental alternate reality drive aboard a version of the Daedalus was still fresh in his mind. "You think!? Rodney, this is not a game. We're treading on dangerous ground here. Remember what happened the last time we encountered an experimental reality drive? We barely made it home alive."

"Yes, Colonel, I got shot, remember." Rodney replied thoughtfully, "So I will take precautions not to activate anything. I suggest you do the same."

After the door opened, John walked inside. As usual, the lights came on, and the consoles in the centre of the room lit up. He was walking towards a large console in the centre of the room when Rodney stopped him.

"Okay, super gene boy, sit in the corner and don't touch anything until I tell you!" Rodney demanded, his tone laced with humour.

A retort was on the tip of his tongue, but he decided against it. He knew Rodney's sarcasm could be a headache in itself. They had been through enough together to know when to keep quiet. Besides, he still had a headache, and the more peaceful things were, the better he'd feel.

It only took a few minutes before he began to feel bored, so he teased Rodney," So, McKay, did you tell Woolsey what we're doing? Or did you conveniently forget?" However, he wondered what Woolsey would think if he knew what they were doing.

"Of course I did, Sheppard. Do you think I would have come without telling him? Especially since I brought Colonel Catastrohpe along, anything could go wrong at any time."

John wasn't sure that comment was fair, but he did end up being injured on many of the missions his team went on. However, that was because he was a soldier, and it was his job to protect others even if it meant getting injured or giving up his own life.

"So you told him you were bringing me along then?" Sheppard commented from the uncomfortable corner where he was sitting.

"What are you nuts!? Of course, I didn't tell him I was bringing you alone. I'm positive he wouldn't have allowed us to come if I had. Please be quiet and let me work out what this console does."

He fell silent for a few minutes before talking again, "So do you think the other McKay came up with the alternate reality drive from the Ancients' research?"

Rodney turned to face him, and the scientist's expression was one of annoyance." It is a distinct possibility, and unlike him, I don't intend on getting us killed. Why don't you shut up and let me finish what I'm doing!?"

He knew not to push things further this time, so he remained quiet and looked around the lab. It was like many other labs in Atlantis, so John didn't know why this one was any different. Although it was clear the Ancients had been experimenting with dangerous theories, he wondered at what point things would go wrong.

As his eyes scanned the room, he noticed a flashing red light on a corner console. He immediately got to his feet and crossed to the room to see if he could ascertain what was happening. The flashing intensified, and he knew something catastrophic would happen if they didn't act fast.

"Rodney, we need to get out of here now," he said urgently, his voice carrying the weight of the impending danger. A high-pitched sound invaded his senses, heightening the tension.

"What did you touch, Sheppard?" Rodney asked with a hint of frustration, his sarcasm adding a touch of humour. I thought I told you not to touch anything."

Despite the hint of humour in Rodney's tone, John didn't think the situation was funny at all.

"Nothing, Rodney," he replied urgently. For all I know, the light started flashing as soon as we entered this room. So I suggest we get out of here and lock the door so we won't be caught in an explosion."

Before Rodney could answer back, he grabbed him by the arm and dragged him out of the room, and with a thought, he locked the door.

A few seconds passed, and he could hear the high-pitched screech, but then it stopped as suddenly as it started.

"Umm…what just happened?" He asked Rodney in confusion," Was there an explosion? If so, it was an extremely quiet explosion." He looked around, his eyes wide with disbelief, as if expecting to see the aftermath of a catastrophic event, his heart pounding in his chest.

"Yeah, I'm not sure. Shall we go inside and have a look? If we do, please refrain from touching anything. The last thing we need is for you to make things worse."

He rolled his eyes at the annoying scientist, "I didn't touch anything last time, Rodney, so I'm certain I won't this time. I'll go in first just to ensure there's no problem."

"Really! What could go wrong that hasn't already gone wrong? Are we going to find a big purple dinosaur or something?" Rodney asked, his voice oozing with sarcasm.

"Just stay behind me!" He replied with exasperation.

After cautiously opening the door, John stepped inside the lab, surprised that everything was as they'd left it. Rodney's computer was still plugged into the centre console, and the lights came on as usual. The only difference was that the red flashing light on the corner console had stopped. So it was clear something had happened - what he had no idea.

He turned to Rodney, hoping for answers, "What is going on, McKay?"

"I don't know anything more than you at the moment because I've just walked into the room. So, if you'd kindly sit in the corner and stay quiet, I'll attempt to find out." Rodney replied with impatience.

John considered replying, but he knew Rodney well enough to understand the gravity of the situation and let him work, at least for a few minutes.

As Rodney frantically typed on his computer, John could feel his friend's urgency: "Have you found anything yet?"

"That's just weird," Rodney muttered, and if John hadn't listened closely, he would have missed it.

"What?" John asked with frustration, matching Rodney's.

"As far as I can work out, nothing's happened," Rodney replied.

"Nothing?" John replied in complete disbelief. His spidey sense was tingling, and he couldn't shake the feeling that something would go wrong - if it hadn't already. He also realised they couldn't stay in this lab forever.

"Anyway, I think I'll download the data and check it out once we return to my lab; until then, this lab should be off-limits," Rodney suggested.

By this time, John's headache had increased, and his arm was beginning to ache, so he had no problem returning to the city's more populated areas.

"You'll get no arguments from me," John agreed," let's get going."

The moment John opened the door, he caught a glimpse of something out of the corner of his eye. The next thing he felt was a stunner beam to the chest, and just before he hit the ground and lost consciousness, he saw a tall, menacing figure moving towards him, and he felt the familiar feeling of a transport beam envelop him.

TBC…

Please let me know your thoughts.