Alternate Atlantis

Prologue

Dr. Malekin tapped his fingers, chewed his lip, and shimmied in place, about as patient as a small child staring at presents they aren't allowed to open yet. His companion laughed at him.
"I know it's exciting, but we must take every precaution. We don't want to overload the gate. If you're so eager to do something, help me double-check the device; and make sure those instruments are recording properly, or it's all for nothing."
"You've 'double-checked' it twice already," the other scientist complained, though he did start to help. A moment later, however, he decided that was just too boring and activated the device. The sound of it powering up was the only warning he gave the others, who scrambled out of the way before the gate activated, undialed.
They all silently agreed to be furious later. For the moment they were busy staring in wonder as the gate disengaged and seconds later was reactivated by an incoming wormhole. As one they turned to the leaders on the project, seeking to confirm just how far that wormhole had come to reach them. Before anything could be said, however, they were all distracted; by four people stepping through the gate.
The scientists called for security and shrank back in fear; except for Dr. Malekin, who slid down the banister from the upper level and strode fearlessly up to the armed strangers.
He pointed to himself and rattled off his full name. "Dr. Locura Evan Momiji Fox Vader Rudolfo Tiberius Malekin. Welcome to Atlantis."
"Loki!" someone hissed sharply, but he took no notice.
"How 'bout you get the big gun out of my face and tell me who you people are?" The leader of the strangers didn't lower his weapon, but did introduce himself as soldiers streamed in to take them into custody.
"Lieutenant Colonel John Sheppard."

Chapter One

McKay paced the familiar cell they had been placed in, reciting various explanations for their situation while the others only half-listened; or, to be precise, while Teyla and Sheppard half-listened. Ronon was sitting in the corner, and either he was faking lethargy to fool their captors or he'd actually fallen asleep with his eyes open. Sheppard was very curious about this, and every so often would flick small objects at the Satedan looking for a reaction. When he had nearly exhausted the contents of his pockets he changed targets, launching a pen cap at his ranting scientist's temple.
"Easy, Rodney," he drawled. "Let's not get all worked up until we know more about what's going on."
"How exactly am I supposed to take it easy? We're trapped in our own cell and surrounded by menacing guards!" One of the 'menacing guards' looked up from her crossword and snickered. "They're not exactly forthcoming with information."
"No, but she looks like she's got something to say."
Rodney hadn't noticed the woman who had just entered, though her hair alone should have caught his attention. It was a bright copper color, streaked with red and gold. The jacket of her uniform was open, revealing a t-shirt emblazoned with a donkey and the words 'I Could Kick Your Ass'. She looked like a teenager stuck in a body 15 years too old for her.
One of the three guards hesitantly approached her. "Um... Colonel..." Another, with less respect for her superiors, stifled a laugh before speaking.
"Hey Freddy, I thought Dr. B talked to you about looking so casual in front of anyone outside the expedition."
The redhead rolled her eyes. "Well, Captain, I know he and I have both talked to you about addressing us appropriately in front of strangers. How about a little respect?"
The captain snapped to attention and replied with mock sincerity. "Yes sir, Colonel, sir." Her superior rolled her eyes again, but did up her jacket and hid her hair under her cap before approaching the cell.
Her eyes scanned them all before settling on Sheppard. "Now that I'm all proper-looking," - she shot the other woman a look - "I'm Colonel Freddy Coy, military commander of Atlantis. Apparently you told the security team that this is your city."
"That'd be because it is. I'm the military commander, Colonel John Sheppard, and this is my team." He introduced each of them in turn.
There was a long moment of silence as she eyed him thoughtfully, until finally she nodded. "Ok, here's the story. We're inclined to believe you are from Atlantis - in another reality. Unfortunately, the machine that was supposed to prove where that wormhole came from didn't work right, and at least one of our enemies might be capable of pulling off a trick like this to get his people into the city. Luckily for you the whole nerd squad is working on proving who you are, and it shouldn't be long before we can either let you out, or dump your flayed carcasses on Genii land."
McKay had been muttering constantly under his breath, either still rattling off theories or questioning the ability of the 'nerd squad' to figure anything out. Now he interrupted himself to address Coy.
"Genii? You think we're Genii?"
She shrugged. "Why not? Sure you don't seem to fit the part, but Arsenault's clever. You're nothing like the team we know he'd want to trust with a mission this important, so you're exactly who he'd send."
Sheppard looked over his team, then back at the other colonel. "I think we may have just been insulted."
She smiled at him. "Not at all. Arsenault judges people based on his personal prejudices rather than their abilities. He only wants straight white men with no personality to speak of, smart, but not very imaginative, with plenty of loyalty but no morality."
"In that case I'll take it as a compliment."
"Well that's how I meant it." She smiled again, locking eyes with him. Behind her back the disrespectful captain rolled her eyes and mouthed 'flirt'. Without turning around, Coy told her to shut up.
"I didn't say anything! Did you guys hear anything?" Guards and prisoners alike shook their heads, though Teyla and the quiet guard were smothering laughter at the good-natured teasing. "I think you're hearing things."
"You don't have to say it out loud."
"So you're a mind reader now?"
"Best friend. It's the same thing." The friendly bickering suddenly came to an end when the colonel's earpiece emitted a sharp squeal. She ripped it off and stared at it like it had bitten her before cautiously raising it to her ear again.
"Liam? I thought you fixed this thing for me. ... Loki? It's your fault then, fix it again. Anyway, you find something? ... Great. We'll be there in a few." She pulled the earpiece away just as it shrieked again. "Good news; we don't have to kill you. Apparently another device accidentally recorded the data that proves your wormhole came from another reality. Which means you aren't enemies, just strangers, so you get to come out of the cage and meet our leader."
She opened the cell and motioned for the three guards to accompany them. Ronon, it turned out, really had been asleep; the bratty captain got her comeuppance when she prodded him awake and he reflexively pinned her to the floor, twitching his trigger finger before realizing he wasn't actually holding a gun. His teammates were very aware of how badly things might have gone if their 'captors' hadn't been so good-natured, but after a tense moment they simply laughed it off. At a nod from Sheppard, Ronon helped the young woman to her feet and they were on their way.
They were too large a group to use a transporter, so there was ample time for Sheppard and his team to study their escorts.
Colonel Coy might have been casual in appearance and attitude, but she had an air of authority that kept them from doubting her command. Most of the people they encountered in the corridors offered the group a greeting, but many also singled her out specifically. They all used her first name, and she soon gave up on pointing out that they were with guests. Instead, she gave the strangers permission to call her Freddy as well.
She refused to say what it was short for.
The other woman was Captain Celeste Everton. She seemed to feel a need to taunt, tease, or otherwise irritate the entire military staff of Atlantis, especially those superior to her. She and Freddy were more surprised than anyone that they had become friends.
The others were Captain Caleb Aryae and Major Zephyr Hale. Hale was a solemn, traditional man trying very hard to ignore the fact that no one around him seemed to care about military regulations. Caleb - there was something about him that made his first name seem appropriate - was a soft-spoken young man who limped occasionally and seemed uncomfortable when anyone looked at him. From the worried glances of his colleagues, this seemed to be unusual. When they reached their destination Freddy looked sternly at him.
"Caleb..."
"I know." He stared at his feet. "I have an appointment for tomorrow." Freddy's gaze softened.
"In the meantime, talk to Liam and your sis. I have a feeling they might be more help than any doctor. Go on, we can handle this." He nodded and left.
Teyla, concerned even though they had just met, asked "Is Captain Aryae injured?"
Freddy shook her head. "Not exactly. He... he had a mission go very wrong. He's having some trouble adjusting, but he'll be alright. He's stronger than he seems. Now, let's not keep the boss waiting." She ushered them into an office, leaving the remaining two guards outside.
Dr. Alastor Bhogavati was not what they would have expected. His Indian surname contrasted with skin dark as ebony and, when he introduced himself, a British accent. Taller and more muscular than Ronon, with a shaved head and beady eyes, he looked more like a bouncer than a diplomat.
There were two plush chairs on either side of the room, and he gestured for them to take a seat. The chair directly in front of his desk had been turned around and was occupied by one of the scientists from earlier, who introduced himself as Dr. Liam Payne. The one who had first greeted them - Dr. Malekin, or Loki - was sitting cross-legged on the desk itself.
Dr. Bhogavati rose to his full considerable height and smiled warmly at them. "To begin, I feel I must apologize. I'm afraid it is our fault you are in this position. Our science team was conducting experiments in travel between realities. As I understand it, the gate on your end should have opened without dialing, closed seconds later, then repeated the process with an outgoing wormhole. That first connection should have included a broadcast message warning anyone on the other side not to come through."
"We must have dialed in between the two wormholes, and the second one superceded ours. We didn't receive any message, though" Sheppard pointed out. Dr. Payne glared at his colleague.
"That would be because somebody got impatient and initialized the experiment before we had recorded our message." Loki stuck his tongue out at Payne.
"Sure, one little problem and everybody blames me. The test was a success! You should be throwing me a parade! We work out a couple of bugs, record your all-important message, and we're ready to start collecting data. Can't do any of that while I'm stuck in here, though."
Bhogavati frowned at the young scientist. "For the moment, your only task is to find a way to send these people home. You are responsible for their predicament, you are responsible for getting them out of it." He addressed Sheppard again. "Our entire science department is working on this. We have the ability to contact other realities, but not to target a specific one yet. Until we do, aiding you will be our top priority. We truly regret that this has happened."
McKay opened his mouth, probably to insult their science team's ability to come up with a solution, so Sheppard cut him off. "Dr. McKay would be happy to help."
Bhogavati nodded. "Very well, he can work with Dr. Malekin." Every one of McKay's teammates was grateful they weren't part of the science team that would have to deal with both him and Loki. "For now, however, I must insist that you see our doctor for a full examination. Standard procedure for newcomers on your Atlantis as well, I imagine. I will have temporary quarters prepared for you. We may speak again later, but I'm afraid I have other business to attend to. Colonel Coy, have Major Hale escort them to the infirmary. Your team and AR3 have a mission; you will leave as soon as you're briefed."
Freddy's eyes narrowed, anger transforming her appearance from laid-back to truly fierce. "It's Arsenault."