Some time after Richard Woolsey took command of Atlantis the I.O.A. made the decision to abandon the Pegasus galaxy and the war against the Wraith, planning to dismantle, strip, and then destroy what was left of the city to keep it out of the hands of potential enemies rather than waste their valuable, and limited, ZPM power charges by flying the entire city across the intergalactic void and back into the Milky Way.
Sheppard vehemently opposed this betrayal of the people of the Pegasus galaxy, who had come to depend on both the city and Earth as their one and only hope to ever be free of the Wraith. When it was made clear that the I.O.A. would hear no discussion on the matter, Sheppard secretly began 'losing' supplies and weapons, which quietly ended up in the hands of the Pegasus natives for use when Atlantis was destroyed and Earth washed their hands clean of the galaxy and its problems.
His ploy was successful...up until the time that Woolsey discovered the accounting discrepancies and had Sheppard arrested and sent back to Earth for court martial.
Home Sweet Home...NotEdit
Sheppard returned to the SGC as a traitor to his country and his planet, and receiving very little sympathy from those he had once called friends and allies. The only mitigating voice in his defense was that of General Jack O'Neill, but even he couldn't 'officially' condone his rogue actions. O'Neill would argue the point with the powers that be, but both the Air Force and the I.O.A. were adamant in their prosecution of the case, with O'Neill's influence the only thing keeping it from becoming a true witch hunt.
Meanwhile Sheppard remained a prisoner of the SGC, awaiting what would obviously be a very speedy trial enroute to a long incarceration.
While Sheppard was returned to Earth a prisoner, another SG team member was also disobeying orders in the Milky Way, interfacing with a Repository of Knowledge against standing orders to leave the technology alone. Captain Ryan Stevenson was brought back to the SGC as a patient, only to die a short time later...his mind and body being unable to sustain the knowledge download and physical transformation the Ancient device subjected him to.
To everyone's surprise and shock, Stevenson subsequently revived from his short death undergoing a dramatic transformation. His blonde hair had turned black, as well as other visible changes as he woke up, not Human, but the first newborn Alterra, beginning a cycle of events millions of years in the making.
When the I.O.A. heard the news of his newly advanced physiology, they planned to make an experiment of him, both in hopes of unlocking his genetic advancements as well as plundering the library of knowledge his mind now contained. He, like Sheppard, was now a prisoner on Earth.
With O'Neill's covert blessing, Stevenson escaped the SGC using his newfound powers, freeing Sheppard and taking him along for the ride as they both fled the planet as fugitives. Using Stevenson's knowledge of the stargate system, the pair traveled to the gate center where Sheppard's eyes were opened to the full extent of the Ancient's former territory.
Return to AtlantisEdit
Given the unique capabilities of the 'gate center' Stevenson and Sheppard were able to return to Pegasus and take control of Atlantis in a very one-sided coup. Sheppard had the pleasure of personnaly kicking Woolsey back through the stargate to Earth, along with the rest of the Atlantis contingent that did not choose to stay behind and go renegade.
Once the takeover was successful, Stevenson flew the city away from the planet into deep space above the galactic plane and away from prying eyes before choosing a new planet (Hoth) to take up residence on. The ice world became the temporary base of power for the newfound Alterran empire, which grew rapidly under Stevenson's control, aided by Sheppard and the remaining members of his former team.
Unable to accept the loss of Atlantis and the shame of losing their very own Ancient, Earth and the I.O.A. put together a task force to travel to Pegasus with orders to hunt down and recapture the renegade city. During the operation Sheppard was taken prisoner onboard the Odyssey, commanded by brevet General Carter. He remained her prisoner for a short period of time, enroute to presumeably Atlantis's address, which Sheppard had not given them.
The bogus address he did give them, however, was close to Atlantis's position and well within their sensor range. Stevenson and a team intercepted and overwhelmed the three Daedalus-class battlecruisers, taking down their shields then boarding and capturing the ships, freeing Sheppard in the process.
The New AlterraEditWithout Sheppard's knowledge, Stevenson implanted him with a tiny device that interfaced with his brain and caused him to lapse into a virtual reality testing ground whenever he was asleep...with no memory recall of the events once he awoke.
The testing followed a repetative format, with Sheppard being faced with the same long challenge time and time again, resetting to the beginning each time he died. Gradually he learned what he needed to in order to overcome his personal demons and complete the test...upon which he had a choice.
If, in the simulation, he chose to walk through the blue stargate, a mere few steps away, he would earn the right to be transformed into a Lantean, as several other team members had already done, most noteably Weir and Jackson.
However, if he chose to continue on up the mountain in the simulation and risk dying and being forced to start all over again, he would have the chance to find the Red Gate, which would earn him the right to become an Alterra.
Never Give UpEdit
Sheppard didn't think long over the choice, choosing to go after the red gate and having to reset the simulation many more times before success, passing by the blue gate each time, which offered the tantalizing end to the horrific simulation, but Sheppard wouldn't relent. Upon passing through the red gate Sheppard was 'transported' away from the simulation into an 'end of test' info session with a programmed Stevenson, explaining what Sheppard had just gone through and how it had been accomplished...after which John woke up in bed, this time with him memories intact.
Upon meeting the real life Stevenson shortly thereafter, Sheppard was mildly angry with the liberties Ryan had taken with him...until the Alterra revealed a second reason for the test.
2nd in CommandEdit
Stevenson told Sheppard that he needed to know that no matter what, Sheppard would never give up. And now that he knew that, Sheppard was not only to become an Alterra, but 2nd in command within the growing Alterran hierarchy...informal as it was.
Sheppard's demeanor quickly changed as Stevenson took him on a tour of the Alterra's former domain, traveling to multiple galaxies and making various introductions, filling him in on the many things that he needed to know, as well as giving him a rough shot view of Stevenson's plans for rebuilding.
Not long after Sheppard became an Alterra, the race launched a resumption of the Lantean War against the parasites...one with a much different battle plan and results. After the initial battle over Atlantis, with the city itself flying up to engage in battle, the Alterra pushed the Wraith back to their inner core worlds, with Sheppard leading the charge as the primary war commander, given Stevenson's varied responsiblities that left him unable to directly oversee the campaign.