Disheartened by another unsuccessful search for Teyla Lt. Colonel Sheppard (Joe Flanigan) returns home to Atlantis and immediately senses that something is not right. Further investigation reveals that not only has the city been completely abandoned its systems are all dead and instead of ocean is now surrounded by rolling sand dunes as far as the eye can see. A significantly older looking McKay appears - a hologram with devastating news to relay. A freak anomaly has sent Sheppard over forty thousand years into the future and everyone he has ever known is long dead. But McKay has a risky plan to return Sheppard to the past and reverse a future that went horribly wrong.