Author's Notes: I wrote this for a project in my Geometry class. We had to write a short story that used deductive reasoning. Mine ended up being the longest. A lot of bits are annoying and make no sense, just because I knew that the main audience for this story would more than likely by 99 full of kids who didn't know a thing about the show. Took advantage of this face. If I stole some weird idea from a fic of yours (McKay having a teddy bear or something), don't get mad. I just can't be original.

Cookies to whoever finds the Quantum Leap reference. Super Special cake to whoever finds the SoapGateLantis reference (from LiveJournal).

And, um... I think that's it.

Enjoy.

Mysteries Of Atlantis

A Stargate Atlantis fan fiction by Courtney Greene

It was approximately 3 AM in Atlantis, judging by the 26 and a half hour days on the planet, and Dr. Elizabeth Weir, leader of the Atlantis expedition from Earth, was still awake. She stood alone in the Control Room, gazing at the Stargate, sipping on a glass of water. Something she often did on nights when she couldn't sleep. She knew she wasn't the lone waking resident of the city, apart from several security officers and probably a few of the scientists in another part of the city. But in the control room tonight, she was alone. Or at least she believed herself to be, until she heard a voice from behind her.

"Good morning, Dr. Weir."

Elizabeth spun around to find Major John Sheppard, commanding military officer of the base, standing behind her in a t-shirt and a pair of sweatpants, holding a tub of strawberry ice cream. She sighed. "Major Sheppard. You shouldn't sneak up on people like that, especially at this time of night."

"Morning, you mean," said Sheppard, shoveling some of the pink ice cream into his mouth.

Elizabeth blinked, remembering just how late it was. "Morning, yes..."

"I take it you, too, have been having some trouble sleeping?" Sheppard took a seat next to Elizabeth on the stairs, silently offering her the ice cream.

She gently took the spoon from him and dug into the ice cream. "Hasn't everyone?" she said. "This city does get creepy at night..."

"I know what you mean," Sheppard suddenly looked very amused, "I saw McKay earlier searching the hallways for his teddy bear. He thinks me or Ford snuck into his quarters and stole it."

Elizabeth cocked at eyebrow at the Major. "Rodney has a teddy bear?"

"Yeah," said Sheppard. "You didn't know?"

"No."

"It's name is Ziggy."

"You did steal it, didn't you?"

Sheppard grinned. "Don't tell him that."

Elizabeth sighed and shook her head at Sheppard. Sometimes the people on this base acted like children, and as the ranking military officer, she had originally expected him to be a bit more mature. She quickly realized that that would have been asking far too much of him.

Her brooding on this fact was interrupted by a loud thump and a yelp from another, not too far off section of the city.

With barely a glance at one another, Sheppard set down his ice cream and the two of them ran to the source of the sound. Lying on the floor, unconscious, was Dr. Peter Grodin. Just a moment after Weir and Sheppard arrived, Sergeant Bates and several other security officers arrived.

"What happened!?" asked Bates.

"Dunno," said Sheppard as he knelt down next to Grodin, "heard a noise, came to check."

Weir turned to one of the random security officers. "Go wake Dr. Beckett. Get him here immediately." The airman nodded and ran off.

"He's bleeding," said Sheppard, "from the back of his head. Like someone... I dunno, came up and smashed him with something."

Weir raised an eyebrow. "You think Dr. Grodin may have been attacked?"

Sheppard shrugged. "It's possible. How else would he have a huge bleeding bump on the back of head?"

"Sergeant Bates," said Weir, "None of your officers saw or heard anything before now?"

The officers looked at one another before Bates shook his head. "No, ma'am. Nothing suspicious."

Just then, the random security officer returned with Dr. Carson Beckett, the chief medical doctor of the base. The man looked dead on his feet. "What's happened?"

"Someone attacked Grodin."

Beckett's eyes snapped open. This had gotten his attention. He knelt down next to the fallen scientist to examine him.

"Major Sheppard," said Dr. Weir, "we don't know what he was attacked."

"I do," said the Major.

"He's got some major head trauma," said Dr. Beckett. "We need to get him to the infirmary."

Several of the security officers scurried off as Dr. Beckett continued to survey Dr. Grodin. Sheppard took a step toward Weir. "We need to find out who did this."

"Major - "

"Someone attacked Ol' Pete, here! We must find out who's responsible."

Elizabeth sighed. It was just after 3 AM, she was too tired to argue. "Fine, fine... investigate. I'm going to bed."

"In the morning, then!" Sheppard declared. "We'll get crackin'."

Weir rolled her eyes and turned to Beckett. "Send word if you figure out what's happened, alright?"

Beckett nodded and Weir stocked off to go to sleep.

THE NEXT MORNING

Dr. Weir now stood in her make-shift office, near the control room of Atlantis, accompanied by Major Sheppard. Sitting on the other side of her desk was Lieutenant Aiden Ford, military second-in-command and member Atlantis's chief exploration team (along with Sheppard, McKay and Teyla). Sheppard had turned the lamp sitting on Weir's desk to shine brightly in Ford's eyes. "This is how a real interrogation should be," he's told her. She had been too tired to argue with him.

"Where were you last night at approximately 3:06 AM!?" John asked, startling Weir with his demanding, overly dramatic tone.

Ford raised an eyebrow at his CO. "I was sleeping, sir."

"Can anyone verify that?"

Ford blinked. "Not really, sir."

Sheppard turned to look at Elizabeth, who simply motioned for him to continue.

"When did you last see Dr. Peter Grodin?" Sheppard asked.

"Last night, sometime. I saw him talking to Teyla not long before I went to bed."

Sheppard nodded. "Teyla, hmm? You're dismissed, Lieutenant. And, if you would please call Teyla in."

Ford nodded and grinned as he got up to leave. "Yes, sir."

After Ford left, Weir shook her head at Sheppard. "I still don't think this is necessary."

"Of course it is!" said Sheppard. "Someone is attacking the residents of this city. We need to find out who."

Weir sighed. "If you say so, Major..."

There was a quiet knock on the door as Teyla Emmagan, leader of the Athosian people, entered Dr. Weir's office. "I was asked to come here by Lieutenant Ford," she said.

"Ahh, Teyla!" said Sheppard. "Come in. Sit down. We have a few questions to ask you."

Teyla raised an eyebrow at Elizabeth, who simply shook her head, before taking the seat formerly occupied by Lieutenant Ford.

"Now, Teyla," Sheppard started, "we hear from certain witnesses who shall remain nameless that you were speaking to Dr. Grodin last night."

Teyla nodded. "Yes, I did speak to him last night, shortly before retiring to my quarters."

"Yes, yes," said Sheppard. "Can you tell us what you spoke to him about?"

"Yes, of course," said Teyla. "He was telling me about sweater-vests, but he had to hurry off to meet with the other scientists. To study some of the information about Wraith ships we obtained from the Genii device, I believe."

"Sweater-vests, huh?" Sheppard asked, stroking his chin in a thoughtful, and again overly dramatic manner. "Who do you say he was going to meet with?"

"Other scientists," said Teyla. "He didn't name anyone in particular."

"Of course!" declared Sheppard. He turned to Weir. "Other scientists! Who would want to hurt Grodin except another scientist... another very jealous scientist."

Not for the first, and most certainly not the last time that day, Weir cocked her eyebrow at the Major. "Jealous why, exactly?"

"Jealous of brains, what else would a scientist be jealous of?" Sheppard stated matter-of-factly. He turned to Teyla and smiled. "Could you please retrieve Dr. McKay for us?"

Teyla nodded and took her leave.

Several minutes later, Dr. Rodney McKay, chief scientific advisor to the Atlantis expedition, arrived in Weir's office, looking rather annoyed.

"Elizabeth, Teyla told me you and Sheppard wanted to question me about Grodin..." he trailed off when he spotted the lamp pointing at the empty chair in front of Weir's desk. He scowled. "Oh, you've got to be kidding me."

"Rodney!" Said Sheppard, putting on his drama again, "have a seat. We have some questions to ask you."

"Do I really need to?" Rodney was quickly entering 'whiny' mode. "I mean, I've got some stuff I need to do in my lab –"

Sheppard suddenly frowned. "Sit down, McKay, before I go to the kitchens and find a lemon."

Rodney paled at the mention of lemons and plopped down in the chair with a sigh. "Alright, what?"

"We hear from certain sources that Dr. Grodin met with several other scientists last night to go over that Genni device," said Sheppard. "Were you present at this particular meeting, Doctor?"

"Oh please," said Rodney, "do you really need to be asking me these – "

"LEMONS, McKay."

"Okay, fine!" said McKay. "Yes, I was there. It was Grodin, Kavanagh, Simpson, Zelenka and myself. And yeah, we were taking a collective look at that device."

"Can you tell us approximately what time you adjourned?"

Rodney raised an eyebrow. "No."

"And why not?"

"Because it was late," said McKay, "and I was tired. And I had spent a good portion of the night resisting the urge to violently pummel Kavanagh. I just wanted to go to bed, I didn't look at the time."

"Would you approximate it as being prior to 3 AM?"

"I would imagine so, yes," said Rodney.

Sheppard nodded. "I see," he said, "and you were in bed at the approximate time of Dr. Grodin's attack."

"Yeah, I was," said Rodney. He was obviously beginning to lose his patience with the Major and his interrogation. "I didn't hear about it until this morning." He turned to Weir. "Can I go?"

"No, you cannot go!" Sheppard answered for her.

Weir shrugged her shoulders at Rodney, who reached over and turned off the lamp. "Well, you can at least not try to blind me while you're doing this. I have sensitive eyes, bright light irritates my corneas."

"Well, thanks," said Sheppard, "I'll be sure to add that to my 'list of things to one day use against McKay'."

Rodney scowled, not amused.

Sheppard stared at McKay, attempting to be intimidating but failing rather dismally. "Who did you hear about it from?"

"Zelenka."

"Who'd he hear about it from?"

"I don't know!"

Sheppard spun around to Weir. "Call Zelenka in here." Weir raised an eyebrow at him. "Oh fine!" He turned back to McKay. "You go call Zelenka in here."

"No."

"Yes."

"No."

"Yes."

"No."

Sheppard threw his arms up in the air. "Oh, for the love of – FINE! I'll get him!" The Air Force Major stood up and stormed out of the office, leaving behind a puzzled diplomat and an irritated astrophysicist.

"Now, Dr. Zelenka," said Major Sheppard, boring down over the Czech scientist in Dr. Weir's office, "tell me where you were this morning at approximately 3:06 AM."

Zelenka sighed, looking around the room at Dr. Weir, and Dr. McKay, who'd decided to stick around and watch his fellow scientists be interrogated. He would have McKay's head for this, he thought.

"I was asleep, as was most of the base," he said.

Sheppard nodded. "So you say," he said. He paused for a moment, most likely to add drama to his coming statement. "Can you describe for me, this little 'scientific meeting' that occurred last night between Dr. Grodin, Dr. McKay, Dr. Simpson, Dr. Kavanagh and yourself?"

"McKay was there," said Zelenka, annoyed, "why don't you ask him?"

"Because I want to hear it from you!"

Zelenka sighed. "Fine, alright. Erm... we were going over that Genii device, with the Wraith stuff, y'know," he made some strange hand gestures in the air and nodded at McKay for confirmation, which he didn't receive. He kept going. "Anyway, we were there for a few hours, mostly just McKay and Kavanagh arguing over... I don't know, something or other, they're like that –"

"What about Dr. Grodin," asked Sheppard. "Did he get in an argument with anyone?"

Zelenka nodded, "well, Kavanagh, of course, but who doesn't argue with –"

"Go get Kavanagh," Sheppard said to McKay, cutting Zelenka off mid-sentence. McKay nodded and exited the office.

"You can go, Doctor," Sheppard said to Zelenka.

Zelenka stood, shaking his head, and left.

Dr. Kavanagh glared at Major Sheppard. Dr. Kavanagh glared at Dr. Weir. Dr. Kavanagh flared at McKay. Dr. Kavanagh just glared at life in general, but that's another story.

"So, Dr. Kavanagh," started Sheppard, "how was your little scientist's meeting last night?"

Kavanagh continued to glare at McKay. "Dandy," he said.

"According to several witnesses, you got in an argument with Grodin."

Kavanagh rolled his eyes. "Right, yeah," he said, "arguments. What, you think I attacked him, or whatever?"

"Answer the question please, Doctor."

"Sure, fine," he said. "We argued. As did Simpson, as did Zelenka, as did McKay," he said this last comment rather pointedly, but he only got a spiteful grin out of McKay.

"And," Sheppard pressed on, "we will be speaking to Dr. Simpson in a bit. But right now, I'm talking to you." He leaned in close, applying that extra drama he seemed to really love. "Tell me about your argument."

"What is there to tell?" said Kavanagh. "We're scientists, we argue. It's part of the job, nothing different than usual."

"Except that, according to Dr. McKay, everyone wanted to make violence against you."

"Like the man said," said McKay, "nothing different than usual." If looks could kill, Kavanagh would have killed Rodney quite violently by now.

Sheppard stared at Kavanagh, either in deep thought or pondering going to find a turkey sandwich. "Alright," he said, turning to McKay. "I want Simpson and Zelenka in here, McKay. All of you at once. Go get them. And get me a turkey sandwich on the way back, please."

Rodney blinked. "What am I, your man servant?"

"Yes, now go."

McKay rolled his eyes and left to office in search of his two colleagues and a sandwich.

Dr. Weir cleared her throat loudly to get Sheppard's attention. He jumped, startled, and turned to her, as if he'd suddenly just now remembered she was even in the room.

"I'm going to go check on Peter," she said.

Sheppard nodded. "I'll be here," he said, a bit too loudly, "carrying out justice and all that."

As much as Elizabeth tried, she couldn't help but smile and she left her office for the infirmary.

"I don't understand why he hasn't woken up yet," said Dr. Beckett as he and Elizabeth stood over the still unconscious form of Peter Grodin. "Maybe a plot device or something, I can't be sure. I'm having Nurse MacKenzie run some extra tests, but the results won't be in until later."

Elizabeth nodded and sighed. "I thought this might happen," she said. She turned to Carson, looking only slightly amused. "You know, Major Sheppard has stolen my office to conduct his little investigation?"

Carson nodded, "I heard. Rodney was running around looking for people, earlier. I'm just waiting for my turn, I guess."

Elizabeth shook her head. "You know, Peter probably wasn't even attacked," she said. She paused a moment, and then turned to the Scottish doctor. "This happened in a room that contains a lot of Ancient technology that has yet to be studied," she said. "Is it possible that some unknown device could have done this?"

Carson nodded thoughtfully. "It's possible," he said. "Though, I'm not sure why the Ancients would invent something that clobbered people in the back of the head."

"You're right," she said, "but it could have just been some kind of freak accident."

"Like Rodney and his personal shield device?"

"Precisely," Elizabeth said. "I think I'll go get Major Sheppard and look into this." She smiled at Carson. "Thank you, Doctor."

Carson raised an eyebrow. "No problem... I think."

Elizabeth exited her empty office, quite annoyed. She had returned from the infirmary to find her office completely empty. No Sheppard, no Rodney, no Kavanagh. She really wasn't in the mood for any of this today. Just as she was about to stalk off to find the missing men, she heard a squeal from down below, near the Stargate.

"Get back here, McKay!"

Elizabeth rushed to the railing and looked over to the lower level of the gateroom, to see Dr. Rodney McKay, internationally renowned astrophysicist and leading authority on Stargate technology and wormhole theory on Earth, much less in Atlantis, screaming like a girl and running in circles. He was being chased by one Major John Sheppard of the United States Air Force, a gifted pilot and a mathematical genius, who was holding a lemon slice in each of his outstretched hands and following in circles just behind McKay.

"Stop it!" shrieked Rodney. "I swear, I didn't eat your stupid sandwich!"

"You wanna bet on it!?" Sheppard said, in his full on threatening military man voice.

McKay shrieked just as Sheppard was about to catch him, and bolted up the stairs. He paused to look around, and when he caught sight of Elizabeth, he ran toward her and hid behind her.

Sheppard followed closely behind, but stopped in front of Elizabeth, seeing the rather angry expression on her face. He hid the lemons behind his back and smiled his most charming smile. "Why, hello Dr. Weir. Didn't see you there."

"Major Sheppard," she said, "just what do you think you're doing!?"

"Well, erm, I was –"

"Trying to kill me!" accused Rodney, still hiding behind Elizabeth. "You know I'm mortally allergic to citrus! One drop of those things could kill me!"

"Oh, hardly!" said Sheppard. He was about to continue his argument, but Elizabeth stopped him.

"That's enough!" She said. She sometimes felt like a schoolteacher. Now was one of those times.

"Fine!" Sheppard pouted and tossed the lemon slices over the railing. There was a yell from below as the lemons hit some random person, but he chose to ignore that.

"Anyway," Elizabeth said, taking a step to the side so that Rodney was no longer hiding from her, "I wanted to tell you, I may have some new 'evidence' for your 'investigation'." She was sure to use air-quotes on the words "evidence" and "investigation".

Sheppard brightened. "Really!? Such as?"

"Such as," said Weir, "Ancient Technology."

Sheppard stared blankly for a moment. "What about it?"

Weir sighed. "The room Grodin was in was filled with as-yet specified Ancient devices. Something could have been activated and hurt him. It's not like it hasn't happened before."

Sheppard nodded. "Yes, of course!" He grinned. "Let's go have a look see!" He turned to head in the direction of the room, and nearly ran directly into Lieutenant Ford and Teyla.

"'Have a look see'?" Teyla asked, looking quite confused.

"Yes, a look see," Sheppard replied. "We're gonna go see if technology caused Dr. Grodin's injuries. C'mon."

Sheppard lead the way as he, Weir, McKay, Ford and Teyla reached the room Dr. Grodin had been found in the morning previous.

"Now," said Sheppard, "Grodin was lying here," he took several steps into the room and pointed to the ground. "Therefore it must be something in this general area."

He spun around to the object closest to him, which looked like a large piece of machinery. Giving a thoughtful, 'hmmm', he reached out and touched it. It quickly lit up and began buzzing. He pulled his hand away the object, and it just as quickly became inactive.

"Well, then," said Sheppard, "that was harmless."

"Let me see," said Weir. She took a step forward and Sheppard moved out of her way. She reached out and touched the object just as Sheppard had. Only this time, nothing happened.

"There!" Sheppard declared. "That couldn't have been it. You need the Ancient Technology Activation gene to get it to work, Grodin doesn't have that!"

Weir was about to agree with him when McKay chimed in.

"Yes he does."

Everyone turned to stare at Rodney.

"Uh, last I checked, Maple-Leaf Boy, Dr. Grodin didn't have the gene."

Rodney suddenly looked extremely insulted. "I'll have you know," he said, "that the maple leaf is a highly dignified symbol of my country!"

Sheppard scoffed. "Like, what, a beaver?"

"Moose?" chimed Ford.

"Hockey?" Teyla was actually genuinely trying to be helpful.

Rodney just glared at her. "What is with you and the hockey!?"

"Rodney!" Elizabeth stepped in before another argument could break out. "Your point?"

"Oh, yes," Rodney said, settling down, "Dr. Grodin does have the Ancient gene."

"Since when!?" asked Sheppard.

"Since Beckett introduced it with that gene therapy of his," said McKay, "Grodin and I were the only ones he tested it on, I should know."

"Right, fine," said Sheppard. "But this isn't what did it, if it really was some piece of random technology." He reached out and touched the object again, and it again lit up and began buzzing. He turned and smiled at his team. "See? It's harmless."

No sooner were the words out of his mouth that something large popped out of the top of the machine, and swug down smashing Sheppard clean in the nose. He shrieked and jumped away the machine, both hands over his face. "MY NOSE!!!"

Rodney laughed and the other three people in the room actually tried to hold back their own chuckles. "Well, I guess we know what happened, Marcia."

Sheppard frowned, glaring at Rodney. "Where are my lemons when you need them!?"

Before yet another argument could break out between these two, Elizabeth stepped in between them, the constant referee. "Not now, you two. We've figured out what it was that happened to Grodin. He wasn't attacked at all." She turned to glare at Sheppard. "You're little investigation was absolutely pointless."

Sheppard shrugged, one hand still over his nose. "Not entirely," he said, "I got to make lots of people uncomfortable. That's always fun."

Weir rolled her eyes. "I'm going to go to the infirmary and tell Carson. Major Sheppard, you should probably have your nose looked at."

Weir left the room, followed by Sheppard. Ford also followed after them. McKay stayed behind, however, to just glare at the random angry machine.

Teyla stood behind him, and tilted her head thoughtfully. "What is it, Doctor?"

McKay turned to her. "Why would the Ancients invent something that just hits people?"

Teyla shrugged and smiled. "One of the many mysteries, the answers to which we may never know."