Sheppard meets with Lorne's team after a Genii contact misses a rendezvous to provide them with info on the missing Teyla. Sheppard enters the Stargate back to Atlantis… and finds the place abandoned and exceedingly hot. He gets a window open and finds Atlantis sitting in the middle of a vast desert in every direction.
Sheppard manages to raise Rodney on the radio, who asks for a description of the base. McKay then tells Sheppard to go to the hologram room and when Sheppard goes there he finds a hologram of an elderly McKay. The hologram explains that Sheppard's wormhole was disrupted by solar flares and sent 48,000 years into the future. The hologram McKay takes Sheppard to the stasis pods but says they have to wait for the proper solar prominence, in a thousand years.
The hologram explains that things didn't go well after Sheppard disappeared. They found Teyla, dead after having her baby and losing it to Michael. They need to make sure Sheppard returns in time to save Teyla, because Michael used the baby to enhance his breeding program and spread the plague. Michael then disposed of the warring Wraith factions and bred even more hybrids.
Sheppard and the McKay Hologram discover the corridor to the stasis chamber is blocked with sand, and there's no way around. Sheppard suggests he go outside but a sand storm is coming. While they wait for it to clear, the McKay Hologram explains that the IOA was reluctant to send forces to the Pegasus Galaxy but finally gave Carter a new ship, the partially-complete Phoenix. Finally they finished and Carter took the ship out while giving McKay a rest break. Carter ran hit-and-run attacks against the Wraith but Michael eventually lured them into a trap and Carter was forced to go on a suicide run destroying three Hive ships.
Later, the hologram McKay returns to tell Sheppard the sun is running out of fuel and expanding, and the planet will be destroyed in 500 years. Sheppard suggests they use the solar generators and take advantage of the increased solar corona. Sheppard decides to go out in the storm before his food runs out, and maintains radio contact with the hologram. As Sheppard makes his trek, the hologram McKay explains that Ronon formed a volunteer strike force of villagers. They went after one of Michael's hybrid laboratories and met Todd the Wraith. A Hive ship arrives and Ronon and Todd go to plant an explosive charge and destroy the entire facility. The Wraith arrive and Todd holds them off while Ronon plants the charge. With no escape option left, Ronon activated the charges and destroyed the base, Todd, and himself.
Sheppard staggers in out of the storm with his life signs at minimum but manages to revive. The hologram McKay provides him with a crystal of information and prepares him for stasis, but Sheppard asks what happened to the real McKay. The hologram says "he" killed once Atlantis was under new management. Woolsey was in charge and ordered the recall of all base personnel to Atlantis, believing Michael won't launch an attack against them. Keller returned to Earth and McKay eventually agreed to go with her and they became romantically involved. Upon arriving on Earth they both got new jobs but Keller came down with an illness due to repeated exposure to the Hoffan drug. McKay decided to change the timeline but Keller asks him not to erase what they had. McKay continued with the research in time travel, with his sister Jeannie helping him for a while. Twenty-five years later, McKay perfected the research and had to appeal to Major Lorne, now General Lorne in command of SGC. Lorne eventually authorized the experiment.
The hologram McKay has Sheppard enter the stasis pod then shuts down.
In the present, Atlantis gets an incoming wormhole and Sheppard comes through, with the crystal containing the information on Teyla's location. Sam confirms he is who he is and McKay confirms the solar flare. Sheppard takes several teams to the planet and they find a facility with data storage units. Exploring it, they set off a booby trap that brings down the building around them.
(to be continued)