Cross Jurisdiction was Team Atlantis, on Earth in a mostly NCIS setting – now, Team NCIS is going to Atlantis and ends up in the middle of a very Atlantean style problem.

Author's Note: Oh my God, this took me ages to write. I started it, I think, three or four months ago, and it just would not end, would not come together how I wanted it. It is longer than Cross Jurisdiction, and it had a bigger cast, more things to keep track of, a lot of medical mumbo-jumbo. But finally, it's finished, I'm happy, and I finally get to post again after ages and ages!

And here it is, the long awaited sequel to Cross Jurisdiction! You probably don't have to read the first one if you don't want to, but I will have small mentions of what occurred in Jurisdiction. Still, it won't mean much to this story.

It's set about mid-to-late season 5 of Atlantis and let's say, just before the end of Season 5 NCIS.

Warning: There are some dark scenes in this fic. Mentions of suicide, nothing too… you know. But, be warned.

Author's Note 2: I tried to get Ducky and Abby out to Atlantis, but my muse is a stubborn b***h. No matter how I tried, they just wouldn't appear in any way that sounded good and reasonable. And I do so like good and reasonable… as far as it can be in a sci-fi fanfic.

CROSSING THE WATERS

Chapter 1

The lights came on as soon as he stepped into the room, flickering as the room used power for the first time in over 10,000 years.

Corporal Nick Ranger grinned. Then he clicked the light atop his gun off as he swept his gaze across the room, taking in the destroyed Ancient computers, the table with shattered glass atop it, the jagged edges of tubes atop it.

He was no scientist, but he figured it was some kind of lab. An Ancient lab, judging from the way it turned on when he walked inside. He wondered how long it would take Dr McKay to find way to convince the colonel that the alpha site was safe enough for scientists.

Stepping carefully, Ranger moved about the room – only one of many throughout the complex located on the other side of the planet to the Stargate – trying not to step on any broken shards of glass. He hadn't been assigned to Atlantis long, but he wasn't a stupid man. He knew lab equalled experiments and in this galaxy that usually equalled trouble.

He studied each instrument and device quickly but thoroughly, searching with a half-trained eye. Everything appeared dead, long dead, destroyed by some kind of weapon, unless he was off. Which he would readily admit was possible.

But there didn't seem to be anything of use, and, giving one last scan with his eye, took a sigh at the lack of anything interesting – to his eye, at least – and departed the lab.

The lights turned off.

Lieutenant Colonel John Sheppard jogged lightly through the halls of Atlantis, a small grin on his face. The Daedalus had just appeared in orbit over the floating city, with its usual supplies of… well, the usual.

Only this time, there was a little something extra, and Sheppard had practically had to beg to get it brought all the way out to Atlantis. He now owed a lot of people favours, and they weren't going to be small favours either.

The Gate room suddenly appeared, and he jogged up the stairs to find Woolsey already waiting. And the leader of the Atlantis expedition did not look anywhere near as smug as Sheppard felt as the colonel came to a jumping halt beside him.

"Looking forward to this then, Colonel," Woolsey noticed in that voice of his that actually neared dry and not as stiff as he stood.

Sheppard nodded. "I've been trying to get this to happen for a month," he told the shorter man.

"I can't believe you actually managed to get this to happen," Woolsey muttered. "Going over my head, I might add."

Yeah, he did feel kind of bad about that. But despite the fact that Sheppard had saved his life, Woolsey was a stickler for the rules. "Just following procedure, Mr Woolsey," Sheppard answered.

"Since when is having a bunch of civilians here procedure, colonel?"

Sheppard glanced at him. "We have civilians here all the time," he pointed out, trying not to be smart about this. But learning that he actually had some pull back on Earth was a small thrill, however small that pull was.

Woolsey finally looked at him, knowing exactly what smart remarks Sheppard was not saying. "But not civilians that only know about Atlantis because they arrested you, colonel."

Oh, low blow. Sheppard winced, turning away. "Actually, they found out because they saved my life. Besides, our men really do need some investigative training."

"From these people?" Woolsey demanded. He sighed heavily, but Sheppard interrupted him before the balding man could go on.

"Most of our soldiers are marines. They take care of marines. Besides, the fact that they do know means we don't have to initiate any more agents into the whole intergalactic secret thing."

"All of which you told General O'Neill, I know," Woolsey muttered. He shook his head. "There's no point talking about this anyway. Are you going to partake in this training, colonel?"

Sheppard shook his head. "No, I'm just supervising. One member from each team. Rodney's ours. More wanted to, but I don't think we'd have the time, or the resources." A surprising amount wanted to do it though. Way too many people watched CSI for them not to want it. He had had to turn more than a few people away. "And a small amount of scientists, who can be pulled away from their own research to do this training."

He looked down at Woolsey, sort of feeling sorry for the man. "It's only three weeks," he allowed. "They won't be disruptive. I'll make sure of it."

"See that you do that, colonel."

Their conversation was cut short there by Chuck leaning over the banister above. "The Daedalus is ready to beam them down now, sir."

Woolsey nodded. "We're ready to receive them."

A second later white light filled the Gate room, slowly merging into four people standing before Sheppard and Woolsey.

And those four people slowly merged into four gobsmacked NCIS agents as they took in the sight around them.

Wait, make that three gobsmacked NCIS agents and one trying-not-to-looked-stunned team leader.

McGee dropped his bag as he looked around, and it thudded against the floor with his jaw as he took in the soaring roof, the sleek architecture, the advanced machinery and the Stargate behind them.

"Wow," DiNozzo muttered, eyes wide, a small smile on his face as he looked up at the control room, seeing the technicians lined there, but missing them as he looked at the building itself. "I mean… wow."

Ziva took a step back, and Sheppard grinned as he watched them, circling on the spot, trying to take everything in at once. He gave a small chuckle, and stepped towards the team, holding out his hand for the only NCIS agent who had managed to maintain some composure.

"Agent Gibbs, welcome to Atlantis."

Gibbs shook his hand, and Sheppard smiled as he realized just how awed the older man was. But he managed to hide it well. There was only the small flickering of his eyes that gave him away, as he too tried to take everything in at once.

And then he looked back to Sheppard, nodding with respect. "Colonel Sheppard. You got any coffee around here?"

DiNozzo finally slammed back to Earth… er, Atlantis, when he heard Sheppard laugh. The man looked happy – and a hell of a lot healthier than he had the last time they had seen the colonel.

Then again, the last time they had seen him, two months ago, he had been shot and nearly turned into a bug. Again. Trying not to think about it, DiNozzo stepped back up, seeing from the corner of his eye as McGee picked his bags back up.

Sheppard, still grinning – apparently at something Gibbs had said, which just didn't follow – turned to the three of them and nodded, before stepping back to stand next to a shorter, balding man who didn't look quite as happy to see them.

"Mr Woolsey, these are Agents Gibbs, DiNozzo and McGee, and Officer David. Guys… this is Richard Woolsey, commander of the Atlantis expedition."

Gibbs shook his hand, but DiNozzo was still trying to come to grips with… well, to be honest, with everything. He had only just gotten used to space travel, or rather, hyperspace travel, whatever the hell that was.

McGee had tried for three weeks to explain it, with no luck.

In any case, Tony had only just gotten used to that when the voice of Colonel Caldwell had come over the PA and told them they had arrived at Atlantis. And now… greeted with this sight… this… place. He didn't think there was a word he knew to describe it. He thought he would need a lifetime to get used to Atlantis. And even then, it might not be enough.

"Welcome to Atlantis," Woolsey was saying, and DiNozzo tried to concentrate on him. He looked like a strange little man, completely out of his depth. Then again, looks could be deceiving. He didn't doubt that if the man was in charge of all things Atlantis, there was no way he wasn't capable. "And thank you for agreeing to Colonel Sheppard's… training exercise."

Sheppard grinned innocently as Woolsey glanced meaningfully across at him. The agents shared a look, before Woolsey sighed and nodded at them.

"I have other things to deal with, but I will find a moment to talk with you all before the exercises begin," he told them, only a hint of impatience in his voice. "I'll leave Colonel Sheppard to show you around."

He walked off and the NCIS agents watched him leave. DiNozzo snorted. "What a happy guy."

"He's just worried that you're here," Sheppard told them. "Dump your luggage, I'll get a few sergeants to take them to your quarters while I give you the grand tour." He turned and motioned to three soldiers waiting nearby, before looking back at them with a grin. "You'll only have a day or so to get used to this place before we begin the training. So, first stop, the infirmary."

Gibbs looked stonily at him. "We just spent three weeks in space," he reminded the colonel. "I'd say any bugs we had were exterminated."

Sheppard shrugged. "It's just protocol. Any time someone steps on the base from space, or through the Gate, they get a physical. Just to make sure nothing hitched a ride."

DiNozzo shared a look with McGee. "Like what?" Ziva asked slowly, frowning in suspicion as they all started off the platform before the Stargate.

Sheppard gave a non-committal shrug as he took the lead. "Mainly Goa'uld. Don't worry, I doubt any of you are actually host to a Goa'uld, but it's one of those protocols that even I won't break any time soon."

DiNozzo caught up to Sheppard as they entered the strange corridors, with their metallic greens, earth browns and shimmering blues.

"So, how are you?" the agent asked, not looking at the shorter man, unable to keep his eyes off everything around him. "Looks like your shoulder healed up nicely."

Sheppard shrugged again. "Doesn't even twinge anymore," he told the man, rolling the same shoulder for emphasis. He nodded at DiNozzo. "What about you? Any lasting effects?"

There were, but you couldn't see them. DiNozzo shook his head, not about to mention the nightmares involving a certain marine hybrid, before changing the subject.

"Hey, I would have thought the rest of your team would have been here to meet us as well."

Sheppard chuckled as they all rounded the corner. "Ronon and Teyla are off world at the moment, visiting Teyla's people, the Athosians. It's their turn to look after Torren for a while. And McKay… well, he's off doing McKay things. I think he has something planned though."

Heavy footsteps warned them as McGee jogged to approach. "Uh, any chance we get to go… off world?"

Sheppard didn't even slow. "Sorry, but I doubt it. It's not exactly a walk in the park, and if something went wrong…" He looked behind him at McGee's shattered face. "Look, sorry, but just getting you here was hard enough. Woolsey's not about to let me take you off world."

Before McGee could make an argument – though it was doubtful he actually would have – they entered the infirmary, and once again the NCIS agents dropped their jaws in appreciation.

"This is your infirmary?" DiNozzo demanded. Sheppard nodded, looking around as if to spot someone.

"It's better looking than any infirmary I've ever been in," Ziva muttered. John still heard her.

"Trust me," he grinned at her. "It's exactly the same where it counts."

"Sounds like you've spent a lot of time in here," Gibbs mentioned slyly. Sheppard shrugged a little guiltily, but it wasn't him who answered.

"You have no idea," a woman spoke up as she appeared from the next room. "I'd say he was accident prone if he didn't do most of it on purpose."

"Not on purpose," Sheppard defended as the woman came to stand next to him. Tony glanced at her appreciatively. "Just -."

"Accidentally on purpose?" the woman asked with a smile, before looking at the NCIS agents, who had the feeling they knew exactly what she meant. "Hi. I'm Dr Keller."

"She's our Chief Medical Officer," Sheppard explained a little proudly, the comments of thirty seconds ago apparently forgotten.

Ziva's eyebrows rose. "Aren't you a little young to be CMO?" she asked, obviously curious.

Keller looked at Sheppard as if a point had been proven. "You'd think so, wouldn't you? Come on through, and we'll get started. It shouldn't take long."

They all followed her through into the next room where she had appeared from, and gestured to a bed. "All right then. Who wants to go first?"

McGee put his hand up, and DiNozzo took the opportunity to elbow him in the side, making the younger agent double up as the taller man held his head up proudly.

"I'll go first."

DiNozzo's mouth snapped shut as Gibbs stepped forward, taking pole position, while to the side, Sheppard laughed out loud, even more so when DiNozzo glared at him.

Keller's meaningful stare and smart words quickly shut that up. "Jeez, I wonder who that reminds me of."

"Surely you aren't talking about me," McKay suddenly interrupted, walking into the infirmary, a life signs detector bouncing in his hands. He had a sly grin on his face, and Sheppard stood up straight, not liking that look. "Cause I don't elbow anyone."

"No, I am sure you are usually the one being elbowed," Ziva told him, glancing at Sheppard to tell him she knew all too well who would do the elbowing. Despite the look of pure innocence on his face.

"Oh, ha ha," Rodney said, emphasizing it with a roll of his eyes. He looked over at McGee. "Here, catch this."

And he chucked the LSD at the man. Sheppard's jaw dropped – whatever anyone might think, those things did not just pop out of nowhere whenever they were needed – but before he could say anything a hand snapped out to snag the small box before the younger agent could do as McKay had suggested.

DiNozzo turned the beeping machine over in his hands. "What is this? Some kind of computer?"

Sheppard and McKay shared a look. "That depends," Sheppard answered. "How many little dots do you see on it."

DiNozzo looked a little worried as he counted, as if he could sense the tension in the room. "Seven. Why?" He looked up. "What does this thing do?"

"Huh," McKay sighed. "I always figured McGee would be the one."

Sheppard rolled his eyes, wondering where the scientist had gathered that assumption. "Congratulations, DiNozzo," he said. "Looks like you have the ATA gene, the one that allows you to work Ancient technology."

DiNozzo glanced at the LSD. "Is that what this thing tells you?" he asked, completely clueless.

McGee rolled his eyes and snatched the console from his team mate's hand. "No, Tony, it's Ancient technology. It's only working because you're touching it."

DiNozzo grinned slowly. "So… because it isn't working now that you're touching it, does that mean you don't have this very awesome gene?" He sounded like a kid in a candy store.

McGee on the other hand looked like he had eaten a sour lolly. "Looks like," he answered, handing the LSD to Ziva. The beeping didn't start up again, and she shrugged, before handing the console to Gibbs.

The lack of beeps told them he didn't have the ATA gene either, and DiNozzo's grin widened. "Does this mean I'm the only one with this gene?" he asked.

"Out of your team, yes," McKay answered. "But having the gene naturally means exactly squat."

"Well, not really," Sheppard broke in, feeling the start of the old argument. "It means you're much better at using Ancient technology than someone who has it because of the gene therapy."

McKay glared at him. "In any case, it doesn't mean much for you. You're not base personnel, so you won't actually be allowed near much Ancient tech. I was just curious."

Sheppard scowled at that, remembering exactly how impatient that curiosity was. "Yeah, about that, McKay. You couldn't have been a little more patient to find out which of them had the gene?" he asked as Gibbs hopped up on the table and laid back.

"What, and wait for Jennifer's test results?" Rodney demanded with a look of disgust.

"No, I was thinking you could have waited the extra five steps it would have taken to hand the LSD to McGee."

DiNozzo's head snapped up where he was looking over said detector. "What's an LSD?"

Sergeant James Holt was worried.

Not about the trek through the forest. That was all too common in the Pegasus Galaxy, especially on the bi-monthly posting at the alpha site. Making sure the place was secure, Wraith free and safe for any retreat from Atlantis, however unlikely that was, was paramount to the survival of the expedition. And this alpha site was new enough for the majority of the expedition's soldiers to believe in that completely.

So no, the hike through dense brush and towering trees that for some peculiar reason reminded him of his family's winter cabin in Canada… that was not what was stressing him out.

No, in this case it was the man striding along next to him, Corporal Ranger.

Holt had only known Ranger for nearly a month now, so there was no way he really knew the kid. But he knew him well enough to know something was wrong.

The kid kept on half-pausing, slowing his stride for a millisecond before he would continue on walking as if nothing was wrong. But in that millisecond, his whole demeanour would change. His face would become pinched and white, his teeth would grip, and his hands would tighten around their hold on the P90, and the life signs detector.

But he could think of no reason why the usually good-natured man would be so angry.

Trying not to glance at Ranger too often, Holt shifted his own grip on the gun in his hands and looked around, searching the bushes for anything that was there. Not that he really expected anything to be around. The Stargate had been quiet since Ranger had come through with Major Lorne's team with the tools and materials they needed to start on the three buildings that had been planned. That had been nearly three days ago. And they might not have had the satellite system Earth possessed, but Atlantis would have called if anything had appeared on the long range scanners or sub-space.

So there was no reason he should be feeling this anxious either.

He sighed and felt Ranger give him a glare. Not a glance, like he would usually have done. No, it was a full-blown glare.

"Got a problem?" the kid asked with a snap in his voice. Holt frowned at him.

"No," he retorted. "But what's yours?"

"None of your business."

Holt decided to ignore the disrespect, shook his head and kept on walking, not bothering to check on Ranger again. At least, he wouldn't have if the kid hadn't stopped suddenly in the middle of the path.

"Ranger?" Holt demanded, stopping when he realized he was walking alone, and turning around. "What the hell are you doing? Come on…"

He trailed off as he saw the kid taking deep breaths, knuckles white around the life signs detector, face pinched. Holt frowned, a little worried all of a sudden. He had the image of Ranger opening fire on him without warning, and the picture wouldn't clear from his head.

"Ranger, are you okay?"

The kid took another deep breath, and then nodded, though his face was still pinched and white. "I'm good. I'm fine, okay! You're not my mother, don't worry so much!"

"Fine," Holt drawled. "Come on, we've got to get back to base."

And he turned and walked off. After a moment he heard Ranger follow, though it wasn't without a few more deep breaths. And he wondered what the hell was wrong with the guy.

End of today's post, we'll get into the real meat of the story tomorrow, because I have readings I need to do for uni. Until then, good night!