With only 24 hours of power left, and unable to use the Stargate, the Atlantis team must once again save the city from certain doom, while Dr. Weir struggles to survive.
While Carter and the Apollo search for missing city of Atlantis, Sheppard and his team risk their lives on a mission to steal a Z.P.M. from the Replicators.
Ronon is reunited with a group of his fellow Satedans who ask him to leave Atlantis and join them. Colonel Samantha Carter arrives at Atlantis to assume command.
After discovering a crystal entity, the team begins to have nightmares involving Sheppard.
Sheppard is captured by a space-faring race who wish to use his Ancient gene for their own ends.
When a deadly infection causes key members of Atlantis to lose their memories, it's up to Teyla and Ronon to find a cure. But when the Marines begin hunting down everyone and no one remembers why, it's hard to work together to cure everyone.
During a visit to New Athos, Teyla and Dr. Keller find themselves on the run from a primitive tribe of warriors and Teyla makes a shocking discovery.
The team meets a man with extraordinary prophetic abilities, who gives them a dark prediction about Atlantis' future. Meanwhile, they join forces with a Wraith in an attempt to fix the virus Rodney created earlier to stop the Replicators, that has since malfunctioned. Woolsey arrives at Atlantis to conduct an evaluation of Carter's command.
After McKay and his sister Jeanie Miller are kidnapped on Earth, Sheppard and Ronon must enlist the help of the NID to find them.
When a mysterious probe crashes into the city the team is convinced the Replicators have found them.
With a way to finally track the Replicators ships, the Atlantis team must come up with a way to finally be rid of the Replicators once and for all.
The team obtains a Wraith Hive ship after the battle with the Replicators and learn something new about their enemy.
When Atlantis is put under quarantine, everyone gets stuck in a room with another person. While dealing with personal issues, they also try to figure out why there's a quarantine, and how to get out.
While accompanying a princess on a pilgrimage to become queen Sheppard and McKay encounter a familiar foe.
After the death of his father, Sheppard returns to Earth where he learns that scientists have created a human-form Replicator that is now on the loose.
Colonel Carter joins Dr. McKay and Dr. Keller on an off-world mission, to convince the people of a world rocked by earthquakes, to relocate. However, things take a turn for the worst when they are plunged into a sinkhole and become trapped in an old Genii mining facility.
When Colonel Carter invites Teal'c to Atlantis to counsel Ronon, who is up for review by the I.O.A., word comes in that the Wraith have discovered the now fully operational Midway Space Station.
While a disease spreads through the Pegasus Galaxy, Teyla believes the father of her child is trying to communicate with her. While searching for answers, the team comes across a very interesting discovery.
After finding some of the missing Athosians, Teyla plans an escape from Michael's secret facility. Meanwhile, Keller investigates the origins of the Beckett duplicate.
Sheppard returns from a mission and finds Atlantis abandoned and surrounded by sand dunes. He soon finds a hologram of Dr. McKay, who tells him he has come 48,000 years into the future, and everyone is long dead. But the McKay hologram has a plan to save the city and restore Sheppard to his own time.