Stargate Atlantis: How it Should Have Been

Summary: Following the End of Season 8 SG-1 are sent to Atlantis to combat the threat of Wraith, since the defeat of Earth's Enemies in the Milky Way arguably the greatest threat mankind faces. Where AR-1 the up until then Premier Atlantis Gate Team are overshadowed and shown up repeatedly.

Prologue: How it Shouldn't Have Been

Following the establishment of communication between Atlantis and Stargate Command changes were made to the Expedition in order to better protect Atlantis and Earth. And while Doctor Elizabeth Weir would remain the administrative leader over the Civilian science contingent, Major General Jack O'Neill would be given overall command of Atlantis and the Military contingent. Bringing with him reinforcements of many new scientists and even more Marines and Air Force Officers, and most importantly SG-1 fresh from cleaning up the Milky Way of the Goa'uld menace.

Lead by Lieutenant Colonel Cameron Mitchell (or as some would say O'Neill's long lost foster son) as the Team Leader, Lieutenant Colonel Samantha Carter (or the So Hot Not Dumb Blonde according to certain astrophysicists), as The Team Science Expert, Doctor Daniel Jackson (or the guy most likely to die and be resurrected multiple times according to Marine scuttlebutt) as the Team Linguist/diplomat, and Teal'c (Indeed) as the Team 'Muscle' so to speak.

Of AR-1:

John Sheppard receives a commendation for valour under difficult circumstances and is promoted to Lieutenant Colonel but is not given Command of Atlantis's Military – which is mostly a relief but partly rankles having done the job for around a year and grown accustomed to not answering to a superior officer. He continues to Lead AR-1 and granted permission to continue the search for his missing Team Member where they encounter and recruit his replacement.

Rodney McKay retained his title as Chief of Science in name only as O'Neill always turned to Colonel Carter over him. However a few months after reconnecting to Earth he was stripped of his title and publicly demoted to just another scientist and member of AR-1 narrowly avoiding been removed from Atlantis and deported back to Earth following the fallout of Doranda despite the fact it was a joint experiment conducted by him and Carter (although Rodney was in charge as he himself stated repeatedly and noisily), With Zelinka been promoted above him even though for all intents and purposes Carter was now in charge of the Atlantis Science Core.

Teyla Emmagan chose to remain a member of AR-1 and continue to fight alongside those she had grown to call comrades and friends, not just to defend her people from the Wraith but all the peoples of Pegasus. Even as Her fellow Athosians were removed from Atlantis and sent to a new world to rebuild the lives lost on Athos, while grateful for the help given to them by the People of Earth she found herself resentful of been parted from her People many of whom risked their lives in defence of the Ancestors City only to find it denied from them afterwards.

Ronon Dex…was new to the team and hadn't experienced year 1 like the others…he was also…just about the same as Ronon ever was. But coming second best to the former First Prime of Apothsis in terms of been a badass alien warrior was rather a sore spot with him, that had made many a Marine regret mentioning it especially while 'sparring' with the Satedan Specalist.

And so SG-1 pranced around the Galaxy saving it one world at a time while AR-1 was relegated to the sidelines of ignominy like SG-2 through 9 through 17 through 25, Who always play second fiddle to the Great SG-1.

It was Inevitable…

Friends were made but so were many more Enemies: The Genii remained a subversive threat skulking in the shadows, the nomadic Travellers ever weary of this new space fearing race that had sent the galaxy into a frenzy not seen in millennia, the Replicators were running rampant barely pushed back time after time, the rogue Asgard the Vanir lurked ever hiding in the deepest reaches of Pegasus desperate for survival no matter the cost, and the Wraith are neverending…their ceaseless hunger causing them to seek out new worlds to devour.

It was Inevitable…

SG-1 would eventually be recalled back to Earth alongside General O'Neill. For the Milky Way is facing a new grievous threat, Earth is about to be invaded, whole worlds are at risk of destruction, the human race faces extinction at the machinations of the last and most dangerous and cunning of all the System Lords. And only five people, the members of SG-1 lead by O'Neill himself can stop him, defeat his evil plan, and save not just the world, nor the galaxy but the entire universe!

And…Pegasus would suffer. Atlantis and the Expedition attacked on all sides by multiple enemies now their greatest deterrent is missing pushed over the brink of destruction only enduring to suffer the next attack, and the next and the next, from the Wraith to the Replicators then the Travellers to the Genii.

In the absence of Colonel Carter Zelenka fails to come up with a last minute save, a single brilliant idea cultivated under enormous pressure to save the day and the city.

Doctor Weir freely gives her life in the hope she can spare her people the need to give up theirs…a gesture that goes unrequited as her people continue to die in vain.

Lorne, Beckett, Keller, Cadmon, Chuck, Amelia, Heightmeyer, Katie, Parrish, Levine, Kemp and even Kavanagh die needless deaths attempting and failing to fulfil their duty to their friends, and team mates. No noble sacrifices just dead and gone, a waste of effort, a waste of life.

The Daedalus and Apollo are both slain in fiery battle the former taking down a slew of Hive Ships before falling, the latter engaging numerous Replicator Warships before taking a lucky hit from a Vanir Cruiser, their crews and commanders going down with their respected ships like the sea crews of old.

…and…of the 'B-team'…the much abused and used AR-1?

Whether fortunate or not depending on your point of view they found themselves one of the few Atlantis Teams of-world, isolated and unaware of the unfolding oblivion. Having been sent partially as a punishment detail on a 3 day long diplomatic mission to M7G-677 (otherwise known as the lord of the flies world only tamer) AR-1's own personal hell stuck on a planet populated almost entirely by kids. It was almost enough to put even Teyla who possessed the patience of a saint even before meeting and spending extended time with Rodney over a 4 year period of ever having children of her own.

Upon their return to a ruined Atlantis currently been raided by the Genii they decided enough was enough, they were going to re-take their city, they were going to save their people, even those they had already lost, they were going to fight the dangers of Pegasus, the Wraith, the Replicators, the Genii and the Vanir, and this time they were going to win. Screw the Earth, and screw Stargate Command and most of all screw SG-1, this one's for Pegasus and Atlantis

AN: Ever since reading Stargate Redemption written by SkywalkerT-65 I've been itching to write my own take on the go back in time and change the future story, but I also want my story to be distinctive and not a rehash of what someone else's done.

Sorry if this comes across as SG-1 bashing but they do seem to pretty much save the universe on a weekly if not daily basis, just once I'd like to see SG-2 or 17 save the day, I know the show is called SG-1 but in Disclosure I think one of the reason the delegates had a hard time believing the Stargate programme was that Earth had apparently been saved from disaster by a fantastic four style superhero team, if they spiced it up by mentioning some of the other team's achievements, maybe it would have seemed less stylized. And before anyone says the same thing happens in Atlantis with Sheppards team, Sometimes Lorne or Zelinka or Grodin or Cauldwell or Beckett get to be the heroes and save the main team and the day.

This is based on the premise that SG-1 are sent to Atlantis following the events of Siege part 3, and since the Goa'uld's empire has been all but wiped out and Earth has space capable battleships of their own, so long as the Ori aren't encountered, and in this universe they haven't it makes sense that SG-1 would have the kind of skills the IOA would want on the frontlines of the Wraith/Tau'ri war, after all up until the Destiny mission (I'm not a fan of SGU by the way) without the Ori most important events take place in Pegasus. And of course with SG-1's reputation they'd naturally take charge and overshadow the otherwise lead team AR-1 (I prefer this designation to SGA-1 which just sounds to much like rip of from SG-1's name.)

It's not that SG-1 couldn't do all the things cannon AR-1 did, most of the events including Michaels creation, disturbing the Asurans, and various skirmishes with the Genii happen pretty similar to how they were resolved in the series but Inevitably Earth would be threatened, and only they have the needed skills to save everyone and so they return to 'save the universe' leaving Atlantis vulnerable without the five people it now relies on to keep it safe from harm. And so Ar-1 will travel back in time to make sure this never happens, but how they do it may surprise you.

Feel free to offer suggestions, but I know what I want to happen, and what I don't, the only current listed enemy I may switch to an ally are the Travellers who having not encountered Sheppard aren't friends in this time line.