The story of Stargate Atlantis follows the cliffhanger episode on Stargate SG-1's seventh season finale "Lost City", where SG-1 found an outpost made by the race known as the Ancients in Antarctica. After the events of Stargate SG-1 season eight premiere "New Order", the Stargate Command sends an international team to investigate the outpost. Soon, Dr. Daniel Jackson discovers the location of the greatest city created by the Ancients, Atlantis. The story unfolds when the members of the expedition encounter the Wraith, the race that defeated the Ancients ten thousand years ago.
The team learns that a rogue Wraith has acquired several Z.P.M.s to power a formidable new hive ship -- and he is headed for Earth.
The Daedalus arrives to defend Atlantis from the Wraith onslaught, but it may not be enough when the team discovers that an even larger armada is on the way.
A new Stargate team embarks on a dangerous mission to a distant galaxy, where they discover a mythical lost city -- and a deadly new enemy.
Sheppard returns to Atlantis after a mission and finds the city abandoned, all systems dead -- and instead of ocean, sand dunes as far as the eye can see.
Sheppard tries to convince Weir to mount a rescue mission to free Colonel Sumner, Teyla, and the others captured by the Wraith.
Colonel Sheppard finds himself the prisoner of a Genii commander, along with a desperately hungry Wraith who has been separated from his hive.
A new military contingent from Earth is sent to take command of Atlantis and defend it from the impending Wraith attack.
The Atlantis team goes against orders to try and save Atlantis from Replicator control -- and to rescue General O'Neill and Richard Woolsey, who are trapped in the occupied city.
Teal'c visits Atlantis to counsel a headstrong Ronon, who is up for review by the I.O.A. But the two must work together when the Wraith invade the Midway space station in order to reach Earth.
With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.
An unstoppable energy weapon leaves Atlantis under siege after Earth launches a preemptive attack against a very powerful enemy's homeworld.
With a group of Wraith hive ships on the way to Atlantis, the team searches for a place to flee and a way to destroy the city. McKay leads a team to try and activate the Ancients' orbital weapons platform.
Major Sheppard plays a dangerous game of cat and mouse with soldiers who have seized control of Atlantis and taken Weir and McKay hostage.
When Daniel Jackson visits Atlantis, he and Dr. McKay discover a hidden lab that brings a new enemy knocking. The Daedalus welcomes a Wraith ally for a special project.
Sheppard races to an Ancient laboratory to save McKay and Daniel Jackson before Todd arrives to destroy a weapon that has a devastating side-effect. Daniel uncovers the identity of the hostile new species.
Michael and his Wraith faction arrive at Atlantis to propose an alliance, hoping to use the retrovirus to transform their Wraith enemies into prey.
Rodney McKay is stricken with a mental affliction that robs him of his knowledge and memories, causing him to revert to a childlike state.
The team boards the Daedalus when it shows up abandoned in orbit, only to find themselves skipping through parallel universes.
Rodney returns to Earth with Jennifer to witness the triumph of his rival, who believes he has solved the problem of global warming. But when the new technology goes horribly awry, Rodney must help shut down the deadly weather device.
After an Ancient device gives Rodney superhuman powers, his enhanced brilliance is checked only by his impending death -- unless he can learn how to ascend.
A woman is found in suspended animation in Atlantis, and the team is shocked to see that it is Dr. Weir herself, who tells them of her trip 10,000 years into the city's past.
Colonel Sheppard and his team embark on a risky mission to steal a Z.P.M. power module from the Replicators -- but must rely on a compromised Dr. Weir to succeed.
When the team finds an Ancient warship adrift on the edge of the galaxy, its crew still alive, Colonel Sheppard enters their virtual reality stasis to communicate with them.
Floating in deep space with the city's protective shield failing, the team must do all they can to keep Atlantis alive. A radical injury threatens Dr. Weir's life.
The team tries to relax during a mandatory day off, until an explosion leaves three people dead -- and reveals that one scientist is a walking time bomb.