With only 24 hours of power left, Atlantis drops out of hyperspace and is helplessly drifting through space with the Atlantis expedition tirelessly working on a way to save the city. However, with Dr.Elizabeth Weir injured and several obstacles on the way, it may not be easy.
Lt. ColonelJohn Sheppard is captured by a never-heard-before race of technologically advanced Humans known as Travelers, who brought him to help activate a dormant Aurora-class battleship to help resolve the population problems faced with the race's limited number of ships, only to be chased after by Wraith. Meanwhile, the rest of his team tries to find him.
A mysterious illness causes everyone in the Atlantis expedition to lose their memories, which will soon kill them all. However, Ronon Dex and Teyla Emmagan haven't been infected, and the fate of the city truly rests in their hands as they try to convince the team to save themselves.
Teyla Emmagan and Dr.Jennifer Keller go to the new Athosian settlement on New Athos on a routine medical check-up. However, when they arrive, they find the Athosians missing, with a tribe of warriors taking their place. With no way to contact Atlantis, the couple is to survive the night while searching for clues as to what happened to the Athosians.
Dr.Rodney McKay's sister, Jeannie Miller is kidnapped by Henry Wallace, who wants her to rewrite nanite coding to save his daughter's life. McKay's attempts to rescue happens to get him captured as well. They must work on the nanite coding if they're to be released, while McKay's team tries to find them.
With the Asurans undeterred in their effort to wipe out Human populations to defeat the Wraith, the Atlantis expedition now have a means of tracking their ships and destroy them using the newly acquired Asgard plasma beam weapons on their ships. However, their efforts mean that the Asurans have to retreat to their homeworld, only to come back again in bigger numbers. In order to stop them, the Atlantis expedition, Wraith and the recently discovered Travelers must work together to stop the Asurans once and for all.
A Quarantine lockdown leaves everyone in Atlantis trapped, threatening several relationships in the progress. However, some of the team learns that the quarantine lockdown might be nothing more than a false alarm, but it does not matter, as the entire city could be threatened.
Dr.Rodney McKay and Lt. ColonelJohn Sheppard are on a familiar planet, to trade, when the royal family asks them to escort a young princess, Harmony through the forest to some ruins, where she will become Queen. However, on the way, they discover that a Genii contingent is tracking Harmony down, by the orders of one of Harmony's own sisters.
When Lt. ColonelJohn Sheppard's father dies, he and Ronon Dex attend his wake, where the two are confronted by Ava Dixon, and informs them she worked with nanotechnology, and a scientist has illegally created a Human-form Replicator, that is now loose on Earth. Dixon needs their help in tracking it down and destroying it before it causes any more damage.
Dr.Carson Beckett, thought to have been killed a year ago, suddenly appears in front of Sheppard's team's eyes, where he is soon revealed to be a clone created by Michael Kenmore and was held as his prisoner. Cloned Beckett convinces the team to rescue Teyla Emmagan, who has also been held prisoner by Michael. Meanwhile, Teyla is finally reunited with the missing Athosians.
While searching for Teyla Emmagan, Lt. ColonelJohn Sheppard gates to Atlantis, where he discovers he accidentally traveled 48,000 years into the future in an abandoned Atlantis, with deserts replacing the ocean. A hologram of Dr.Rodney McKay comes up and gives him a chance to get back to the present, to prevent a future in which everyone dies.