After flying away from Lantea to escape an Asuran weapons satellite, the hyperdrive shuts down without warning, leaving 24 hours of power left. The Atlantis team must once again save city from certain doom. But as they drift alone in space, the expedition must fend off space's natural enemies.
Colonel Sheppard and his team must plan a daring infiltration to steal a ZPM from the Replicators, power up Atlantis and head to their new home. Meanwhile, Colonel Samantha Carter and the Apollo search for the lost city.
A group of Satedans from Ronon's past enlists the help of the Atlantis team on a dangerous mission against the Wraith.
Sheppard becomes host to an infectious energy form after touching a crystalline growth during an exploratory walk on a jungle planet.
Sheppard is taken prisoner aboard a rogue ship run by a ruthless human commander.
After a virus infects nearly everyone in Atlantis, McKay discovers cryptic letters and has no recollection of his identity.
Teyla and Dr. Keller arrive on New Athos and discover that the entire settlement has been abandoned.
While searching for her people, Teyla and the team meet a man who predicts a frightening future for Atlantis.
After McKay and his sister are kidnapped on Earth, Sheppard and Ronon must find them, with the help of the NID.
When a mysterious probe crashes into the city, the team is convinced the Replicators have found them.
After being armed with the means to track Replicator ships throughout the Pegasus Galazy, the Atlantis team works toward eliminating the Replicators.
The Atlantis team salvages a partially damaged Hive ship and retrieves information that may help in their war against the Wraith.
Members of the Atlantis team are trapped in various sections of the city after an alarm initiates a quarantine lockdown.
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.
During an off-world mission McKay, Carter, and Keller get trapped in an underground chamber with no way out.
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.
Following another unsuccessful search for Teyla, Sheppard returns home to Atlantis to find the city completely abandoned.