Stargate Atlantis: How it Should Have Been

Chapter 1) let's do the Time Warp again!

Rodney McKay typed rapidly on a Laptop hooked up to a Rectangular shaped Ancient Device set up on a mostly clean and intact desk in one of less explody labs left in the city which may sound grammatically incorrect but was a fair description of the room in question.

Lit only by the light of a few scattered torches and the glow from Rodney's computer screen, the walls were blackened and warped in places some of the pillars were broken or bent at odd angles, the door jammed half-open or half-closed as Rodney would always put it, the floor covered in ash and shrapnel, and the occasional piece of debree.

Still clad in his off-world uniform complete with flak jacket and a handgun lying next to his Personal Computer, Rodney's face was one of supreme concentration seemingly blocking out all external stimuli.

Suddenly without even looking up from his work and still typing one handed he reaches out and in one smooth motion grabs his gun and swings it up in the direction of the door firing a single shot. Dropping the stealthy but obviously not stealthy enough Genii soldier cleanly just like Ford, Sheppard and more recently Ronon had been training him to do.

Dropping the gun back on the desk he continues to type away on his computer as if he hadn't just killed another living, breathing, feeling human being like himself.

"Geez Rodney" John complains as he ducks into the room, not even earning a flinch from Rodney "if that had been Me, Teyla or Ronon what would you have done then?" he asks wryly coming up to peer over the scientists shoulder, not that he could make heads or tails of the display, may as well be written in Ancient or double Dutch for all he was good at math he wasn't a super-genius like Rodney…not that he'd ever admit that out loud.

Rodney pauses briefly to glance and roll his eyes at Sheppards inane question "Pe-lease" he sneers "if it had been you, Xena or Conan we both know I wouldn't have even heard you open in your case your big mouth and start talking" John looks mildly affronted and yet moderately pleased by Rodney's faith in the team at the same time, but makes a mental note to remember that big mouth comment for the next time Rodney shoots of his mouth incessantly.

"I mean" Rodney gestures dramatically with one hand while the other continues typing at a more sedate pace "are these supposed to be their black-ops equivalent? Kusanagi could have taken him out bare handed and she's hardly Ninja class material now is she?" which was a slight exaggeration and stating the obvious, although the image of timid little Miko a petite girl of Asian descent clan in Ninja regalia wielding a Katana in one hand and a brace of Shuriken in the other doing back flips and killing Genii commando's was pretty funny. Thank God she transferred to Mid-Way during the last rotation; so far all evidence indicated that no one had made a play beyond Pegasus…yet.

"Who do you think will attack us next?" John asks randomly pulling back he leans against a mostly upright if leaning slightly to the left pillar "My moneys on the Vanir" sneaky creepy naked aliens, you just couldn't trust them. "We pissed 'em of pretty badly when SG-1 blew up their SWHN" Stargate and Wraith Hyperdrive Negator, they stole and assembled the device about a year ago, just another glorious victory to chalk up to the greatest team since the A-Team. "Of course Teyla thinks were overdue a visit from those travellers looking for tech to upgrade those ships of theirs" he snap his fingers and points at Rodney who continues to seemingly ignore him while continuing to work. "And Ronons betting Wraith but then he always does" he smiles an ironic smile, a dark grin stretching across his features for a moment before it is gone.

"We done yet?" Ronon asks boredly striding into the room side stepping the various damaged Ancient Doodad's as John refers to the wrecked remains of Ancestor Relics littering the floor, practically in every section of the city. Teyla appears by his side as though by travelling through the shadows themselves and he did not jump; even Rodney didn't jump that time…alright maybe a barely noticeable twitch which neither of the Earthers picked up on but judging by the woman's slight smirk Teyla had definitely noticed…Damn it!

John raised an eyebrow at Teyla's silent assassin routine, not that she'd like him referring to her skills in such a fashion, the Athosians are not barbaric murders and only fight to oppose the Wraith and to defend themselves. He was pretty sure she'd unnerved Ronon this time but he couldn't be sure, Damn alien team members why'd they have to be so inscrutable? At least they didn't just say 'Indeed' all the time.

Rodney merely gives Teyla an enthusiastic wave and a lopsided grin his grey eyes twinkling which actually came as a relief for a moment there John thought they were becoming total socipaths, with absolutely no redeeming qualities what so ever…which would be bad what was the point of beating the Wraith if you became even worse than them in the process?

Ronon had seen it happen men willing to sell out their comrades, their friends even family just to live a short while longer, even dropping to their knee's and praying to the Wraith rather than submit gracefully to their fate. Give him a gun and a burial in fire any day.

"We have…discouraged the Genii from patrolling this area" Teyla states diplomatically which was code for them having killed each and every weapon obsessed foot soldier come across with extreme prejudice.

"So how many did you guys get?" John asks childishly, it always came down to a competition with him.

"Twelve" Ronon grunts irritably it was as if they were purposely avoiding him, the cowards!

"Thirteen" John crows triumphantly, although admittedly beating Ronon at anything combat based wasn't anything to take lightly.

"Fifteen" Teyla did the Athosian eye-brow thing at Johns disappointed 3 year old act while Ronon merely looked amused that their fearless leader hadn't won either. There was no shame to losing to a woman, especially if that woman could kick your ass seven ways to Sunday.

"One" Rodney speaks up carelessly from his work causing the team to stop and stare at him questioningly. Rodney sniff's and shrugs glancing back over his shoulder "what?" he asks irritably "you did ask" he states of-handedly.

"I don't think you stood much of a chance Rodney" John replies tactfully which is to say not very.

Teyla sashes over towards Rodney offering John a mischievous smile two can play at that game, and having spent four years working with these Earthers who any half-way civilised Pegasus World would class as inherently insane and had picked up a few things like this.

"That was most impressive Rodney" she brushes her lips over his right cheek in a chaste kiss causing the flummoxed scientist to freeze for a second as his brain struggles to process what his body has experienced, a light blush appearing on his face which was mostly hidden by his back to the others.

"Th-thanks Teyla" Rodney stutters nervously his typing reaching a new crescendo as he apparently tries to bury his embarrassment in his work.

"I thought we decided you'd won" John complains almost but not quite like whining that was McKay's niche after all.

Teyla smiles innocently at her team mates "then as the winner is it not my prerogative to choose my prize?" she asks vaguely.

John looked like he'd just seen someone kick a puppy. While Ronon's eyes bug out slightly as he glances from Teyla to Rodney speculatively with new eyes. And if Rodney got any paler he'd faint…uh pass out.

"Oh I see again with the mocking and just when I'm working on our game changer as well" Rodney grouse "do you have any idea what the consequences would be if even a single digit of my very complex calculations is incorrect? Huh?" he did and it wasn't much of a comfort to know that it was more than likely that they would cease to exist.

"Yeah, yeah we all die and the universe goes kaplooie" John replies dismissively not fazed at all by his team mates complaints after all when it came to Ancient Tech if McKay couldn't do it then it couldn't be done case in point for Carter and Rodney's Sister's Matter Bridge project. "What you got?" John asked screwing up his eyes to squint at the inocules looking Ancient Device hooked up to the Laptop they'd scavenged from the remains of Carter's personal lab.

"I was able to recover it from Janus's lab fortunately he built his secret mad scientist lair's to last so it survived the attacks in relatively good shape" Rodney explains with a wishful expression present on his face. He'd kill to have his very own secret evil genius lair to plot and scheme mad science in…heck a personal lab of his own instead of having to share with Archimedes, Coleman and…shudder…Kavanagh.

"My esteemed colleagues" they could practically hear the sarcasm dripping of his tongue "including the great and wonderful Samantha Carter herself" okay now they could hear the sarcasm drenching every word "have wrote it of as a mere prototype time machine, another one of the Ancients many overambitious failures" and to be fair most powerful ancient devices generally were…tumour creating weapon anyone?

"And it isn't and doesn't?" John asks wearily, hoping he was wrong Time Machines were cool.

"Actually it is a prototype Time Machine and it does in fact work" Rodney announces smugly, teach that dumb blonde bit to deny him access to the cool toys, he could have figured this out a year ago never doubt Rodney's superiority with all things Ancient.

"Doesn't look that impressive" Ronon notes uncaringly earning a glare from Rodney, It was an Ancient Device that could literally tell the laws of physics as we understand them to go fuck themselves for Einstein's sake! And a disapproving glance from John, didn't he realise the coolness factor of Time travel?

"What are you kidding?" Rodney snarks "this is the holy Grail! Well as far as were concerned anyway" he muses "Janus based a lot of his time travel research on a failed Ancient Project that took place millions of years before Atlantis left Earth, it was his passion, his obsession and we know that with the advances in technology the Acnients had made by the time they reached Pegasus…"

"He succeeded" Teyla finishes cautiously "our meeting the alternate version of Doctor Weir is proof of that" she comments glancing at her team mates carefully.

Rodney nods his head wildly in agreement "eventually he devises Temporal Transference Technology that when hooked to a Jumper can physically send you backwards of forwards through time"

"Triple-T?" John snorts at it "your making that up" he announces teasingly earning a sneer from Rodney who treats his interruption with the haughty contempt it deserves and completely ignores it.

"But" Rodney holds up his hand "before he built his first viable Time-Jumper" John and Rodney exchange smug glances at the phrased name, only slightly confusing their Pegasus native companions who are more or less used to it "he developed this device which works more like the original Time Machine discovered on P4X-639 in that rather than wrapping a physical object in a temporal bubble and sending them through time like a hyperdrive only moving through time instead of through space" Rodney explains using laymens terms how the Time-Jumper works "it instead sends a person through their own timeline, for us it'll appear like time's been reversed which is actually impossible but it'll look like it"

"And since only those who have used the device remember the previous timeline and have knowledge of the future they can change the past and therefore the present and the future" John states coolly "what I've seen Back to the future and read comic books like any other guy" he protests finding every ones blank gaze at him disconcerting.

"Closet Geek" Rodney mutters irritably not realising the irony of that remark "but in essence that's about it"

"If it's that simply why didn't he use it to defeat the Wraith" Ronon asks simply, someone always has to ask the awkward questions but really it was a good point.

"That is true" Teyla sighs "didn't he use the device himself in order to save his own people?" she asks hopefully, it just had to work Rodney promised he could fix it and that all this wouldn't be for nothing.

"Are you kidding?" Rodney demands miffed that they doubted him "of course he used it, several times according to his hidden logs but what you have to remember he was one man, and had to keep his real research hidden from his peers, and superiors time travel been among many other things to be one of the Ancients great taboo's probably due to their previous failure to master the fourth dimension" In many respects the Ancients were so far beyond them it was like comparing modern man to a Neanderthal but in other respects the ancients were so ridiculously narrow minded and stupid it beggared belief. "He couldn't exactly come forward with any of the knowledge he memorized of future battles and events without…"

"Without the Ancestors questioning where he got his information from" Teyla finishes solemnly no longer holding the misconception many of her people had once held about the Ancients, they were just as fallible as any human being after all, and that fact made her feel closer to them than ever before.

"Hmm" McKay shrugs his shoulder "I'm not sure what the Penalty would be but it wouldn't be a slap on the back I can assure you the only reason he got of without punishment ten thousand years ago when Elisabeth showed up was because they'd just lost the war and were about to abandon the city for Earth" although he wouldn't put it past them to remember the incident for when they were all safe and sound God knows how he got away in order to build another one found in the Milky Way. "In any case I'm sure he tried given hints and advice but uh it probably didn't help that he was considered to be quite the maverick as far as ancients go, always pushing projects on subjects the ancients frown upon or have outright declared illegal" shakes his head bemusedly if only Carter had listened to his plan to use Replicator technology against the Replicators just 'cos she had bad experience with a robot stalker who created an evil robot version of herself was no reason for her to turn down his idea without a second glance "since he was basically on the high councils shit list no one and especially among the military caste took him seriously, he was a scientist not a soldier after all"

"Kind of sounds like you" Ronon comments casually.

"I suppose" Rodney replies seemingly flattered by the comparison. Janus was after all one of the few Ancients known to actually care about Humans rather than just treating them like a colony of ants in an ant farm to be tossed away when you become bored with ants.

"I believe in one of the timelines" Rodney continues distractedly "he focussed on research that would later lead to the creation of the Aterrio Device I also believe he used his acquired knowledge to give his fellow 'Mavericks' so to speak a helping hand of sorts" He shudders in revulsion "ultimately leading to the creation of the Exogenesis machine and Charybdis" Sg-1 my have taken the lead in dealing with the former Ancient Doomsday Device but it was his team that had got caught up in the fractured realities that were succumbing to entropy due to the actions of an ancient super-genius teenage computer program with a superiority complex and a startling resemblance to a certain Air Force Colonel.

John makes a face "remind me to thank him for that" he remarks darkly. So much for the Wraith half the time it seemed like one of the Ancients over ambitious mistakes would end up destroying the whole universe case in point for Replicators. "I'm not an expert or anything" John drawls in his but I could have been in mensa and do know a thing or to tone of voice "aren't we in danger of starting a never ending series of groundhog day style time loops?" repeating today was not high on Johns list of things to do as it was sandwiched between Been fed-upon by a wraith and mind-probed by a Replicator.

"A design flaw" Rodney states dismissively "one Janus was able to remove in his prototype, for one it's a complete standalone system not requiring a connection to the Gate Network to function and it's designed to burn out after use so it's a one way journey and most importantly no one who comes along after you can use it" he smiles smugly "time loops cannot form because the connection to the device itself is broken after the initial time jump" Janus had made use of it to gain some 'borrowed' time so to speak he just couldn't come up with a way to defeat the Wraith that could be pulled of by a single man. This was why Rodney needed his team to go with him as together they could accomplish what one man couldn't and win.

"Janus actually had to rebuild the device after each use sent him to the past naturally after each successive jump he grew quicker at designing and assembling the device and any of his other equipment designed in a previous timeline" Which actually meant if they screwed this up they'd have a lifeline so long as they could reach Janus's secret lab in Atlantis as he had gone back to a point before he created the time machine while they would go back to a point before it's discovery. "His mistake was there is no immediate fix it for the Wraith of for anything in life" he snaps his fingers "but we've proven it's possible to out trick and out manoeuvre and generally mind fuck our enemies until they don't know which way to turn" he smirks confidently at his team mates "the Ancients were idiots" he states matter of factly as if He hadn't just referred to the most technologically advanced race known to man as morons "they tried to fight the Wraith in an all out war, matching ship for ship, battle for battle even after they realized they were hopelessly out numbered…but we're smarter than that, and…sneakier"

"Guerrilla warfare tactics, sneak attacks, hit and run strikes…" John nods his head in agreement a slight smile on his face "could work"

"Sounds good to me" Ronon claims it was after all his speciality.

"If we could reduce the Wraith to more manageable numbers…" Teyla tails of in thought. "We would be able to best them in a conventional war" she realizes.

"Well that would take us some time maybe decades but yeah" Rodney smiles happily "it would be extremely, extremely hard for the four of us to pull it of…nearly impossible I'd say" he announces casually under the bemused gaze of the team "so it shouldn't be a problem for us isn't our motto: we make the impossible possible?"

"I thought it was always look on the bright side of life?" John replies teasingly.

"Very funny" Rodney replies turning back to his laptop he types in several more commands and laughs "and we're…set!" he announces gleefully "I'm afraid the maximum range is a decade so we won't be able to go back any further than that" the Second year of the Stargate Programme, could be worse, they should be able to avoid the SGC's attention both on and off-world long enough to make a break for Pegasus. It was just to bad they wouldn't be able to pick up any of their old friends like Elizabeth, Beckett, Lorne and Cadmon, not that traitor Zelinko, but it would have been nice to see Miko, Grodin and Katie again.

"Are you sure we can't just go five years back to just before we leave earth for Atlantis?" john asks trying not to whine, while not as low on his list as repeating the day over and over, repeating the last five years of his life before Atlantis wasn't exactly in his top ten most wanted things to do list.

"Yes" Rodney declares firmly turning back from his computer "I've thought this through Janus's problem was lack of forethought I mean…he was a brilliant scientist a certified genius but uhm, he was how should I put this…Zelenka" His team mates exchange confused glances at each other and Rodney who sighs "he was more a poke it, prod it, stick some calcium carbonite in to see how it reacts rather than a cautious lets take some readings and see what's going on kind of guy" john mouthed oh as he saw where this was going "Which was one of the reasons why he was so unpopular among the Ancient lab assistants in Atlantis actually" otherwise his 'maverick' status would have been considered 'cool' by Ancient youth sub-culture. "They tended to dislike the random electric shocks, and burnt hair that was part of the job description.

"Zelenka" John confirms amusedly. A talented and brilliant engineer to be sure considered by many to be a genius perhaps not in Rodney or Carter's league but at least close. Even so the man and the engineering team he headed were terribly lax about safety protocols and regulations as several of the newbies assigned to them fresh from Earth had discovered to their peril. Rodney had at one time in between projects tried to prove he and Sergeant Siler were in fact related it was possible through a distant ancestor…just very, very unlikely unless he had a really fast bike anyway.

"At any rate trying to change things like our arrival in Pegasus probably won't work" Rodney claims sadly. "If we don't wake the Wraith on Athos and lets face it we really don't want that to happen again it could have catastrophic effects on the timeline"

"How is me not waking up the Wraith a bad thing?" John asks confusedly.

"And how long do you think it would take before one of our recon teams encounters the Wraith?" Rodney asks sarcastically "Eventually they'll notice that theirs a new advanced civilisation in the galaxy and try to track us down to cull us, then they'll discover we're using Ancient Tech and occupying Atlantis and sooner or later…"

"Earth" John states simply, it was probably inevitable so long as they chose to travel to Pegasus and let's face it there was little they could do to stop the SGC from sending an expedition to Atlantis.

"Surely it would be better if we delayed the Wraith's awakening for as long as possible" Teyla declares firmly "we have already faced the siege of Atlantis once before and survived"

"That's the problem, we only made it last time due to pure luck and Major Kamikaze here" Rodney replies gesturing at the aforementioned suicide mission magnet who merely gives him a wounded expression in return. "With Sumner in charge and if he hasn't been taken by the wraith he may well be do you really think he'll listen to us? Let the Athosians come back with us to Atlantis, serve on our Gate teams?" Rodney glanced at Teyla and Ronon "Sorry but not everyone from our world will trust and believe in you two, not to mention the SGC has declared time travel along with dimensional travel on purpose illegal"

"If they find out we're trying to change the timeline our superiors back at the SGC will try to stop us, try us with treason or something like that" John winces and massages the bridge of his nose. To bad time travel wasn't as simply as they made it in the films where nothing anyone did had any real effect on the person sitting there watching it.

"So we go back further" Ronon states gruffly "I know I won't be able to save Sateda but if I can convince some of my people to come with me through the Gate…" he doubted there would be many who'd listen to a mere Specialist, but if he could get Melena and manage to convince enough warriors to follow him. "We can hit the Wraith with hit and run strikes until you arrive"

"Great, obviously it'll take a while for me and John to reach Pegasus…" Rodney begins but is cut-of by John "that's a bad plan Rodney we can't leave Teyla and Ronon to fight the Wraith alone" he declares irrefutably, refusing to abandon members of his team.

"You didn't let me finish" Rodney retorts snarkly "Obviously we can't use Earths Stargate however give me a few months and I should be able to get us off-world and within a year to Pegasus, where we can meet up with Teyla on Athos, and Ronon and his merry band of men at the alpha site" to bad the Replicators had to go and blow it up in their current timeline, and by that the whole planet had been destroyed.

"That would make a good location for an anti-Wraith fraction to operate out of" John agrees starting to warm up to the idea, he was sure Rodney could get them to Pegasus within half a year tops, but was just edging his bets so Ronon and Teyla don't worry about them if it takes longer.

"I will have to care for my people once again I will not put them in harms way again" Teyla replies sadly "but when Atlantis is rediscovered by the descendants of the Ancestors it would be the Athosians pleasure to assist you in opposing the Wraith"

"Just so long as no one tries to go to Atlantis" Rodney warns them "We can't be sure if the fail safe will even work in the changed timeline, if the shield collapses completely and the city is flooded we'll lose our best base of operations, and we certainly don't want the Wraith seizing it before we've even reached Pegasus" Ronon and Teyla hurry to assure Rodney that they will not even think of going to Atlantis until after he has arrived to supervise everything.

"Well good, I mean we have the locations of a dozen or so ZPM's we can pick up…most of them depleted" Rodney mutters under his breath "if the worse comes to the worse we can always try another heist from the Asurans" since that would akin to prodding a sleeping tiger that would strictly be a last resort option. "We have Gate addresses, names, dates…"

"The mother-lode of Intel, a soldiers dream" John claims coolly, this was so crazy they just might pull it of yet.

"Yeah I'll get to work on things on my end and when I'm ready I should be able to get in touch with you so we can meet up and…well I'm still working that part out" Rodney admits awkwardly.

"I am in the military Rodney" John complains sarcastically "they won't except that I have to visit a friend I haven't even met yet in order to go save another Galaxy as a valid reason for time of!"

Rodney blinks twice and shrugs "Oh I don't know it might do, at least pending a psychological review" he replies haughtily "like it matters in the long run, we're both going to end up AWOL as far as any earth authority is concerned" he declares uncaringly. "Just try not to get killed" he finishes lamely.

"Good advice" Ronon replies wryly.

"I will not fail my people again" Teyla declares.

"So what will happen when it happens?" john asks excitedly, it wasn't everyday you got to activate an Ancient time machine…nope not everyday, every other month, maybe.

Rodney shrugs "I think we'll pass out and wake up in the past we may suffer from disorientation until we get used to been our younger selves, but it should pass, and we should remember everything!" he claims of-handedly.

"Then let's get it over with" John declares moving to stand beside Rodney in front of the device alongside Teyla and Ronon.

"Well cross your fingers or something" Rodney mutters typing a command into his computer.

The Ancient device glows all over with a white bubble of light that washes over the four of them standing in front of it before the universe implodes.

End Chapter

AN: If anyone thinks Rodney couldn't have pulled of that shot, maybe not during the first three years, but maybe during year 4+ and while he'll never be on the level of his team mates I'd like to think he can get the drop on a mere Genii soldier.

This isn't strictly supposed to be an SG-1 bashing fic, but Ar-1 hold some animosity towards them, naturally bitter about been sidelined in favour of the SGC's golden boys and girl. This is especially because from their point of view SG-1 run away and abandoned Atlantis when the city needed them most, and that they should have stayed on earth if that's all they care about.

Ar-1 will be way darker than canon in this bearing in mind they've seen their home destroyed and their friends and comrades killed. They're not psychopaths and still have their morals which won't let them do anything really evil like steal the ZPM from Proclarush Taonas, which will be needed to defend Earth from Anubis. Expect some dark humour from them though.

I haven't got any definitive pairings worked out yet (Teyla was just teasing Rodney and winding up John, giving them a taste of their own medicine) I'm against pairing up anyone in the team together, as that would conflict with their close bonds if someone meant more to one of them than the others. I have a good idea about who to pair Sheppard with and all I'm saying is it is an extremely rare pairing, and perfect for my purposes.

This is set around late season 4 with some differences to compensate for no Ori, and having SG-1 in Atlantis; the Replicators haven't been destroyed (because SG-1 are biased against them and won't let Rodney try to use Replicator technology to come up with a solution), Michael is around and has captured the Athoisans but not Teyla (possibly because she isn't pregnant, since she has been unable to spend as much time with her people she has been unable to form a relationship in this universe.) The Travellers are hostile towards the Tau'ri for some reason. And the rogue Asgard were revealed earlier, possibly due to Daniel living in Atlantis and discovering Janus's lab earlier.

Working on ideas for Future Chapters:

Rodney: We now have shields that can take a Mark 12 detonation at point blank range, a sensor array that could pick up greenfly on a leaf from high orbit, an Intergalactic Hyperdrive only a few specs lower than that of the Asgard, our weapons systems are only outclassed by those designed by the Ancients themselves…and we have a Karaoke bar on C deck.

John: Wow…really?

Rodney: Ha, ha…No!