With a plan to potentially extinguish the Replicator threat, the Atlantis team must seek an alliance with a fleet of Wraith ships.

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.

Dr. Daniel Jackson arrives in Atlantis to investigate a hidden lab left behind by the rogue Ancient scientist Janus. Their discovery has attracted the attention of a mysterious group of aliens, who infiltrate the city. Meanwhile, "Todd" and a delegation arrive on the Daedalus to bring forward Dr. Jennifer Keller's gene therapy.

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.

Colonel Sheppard finds himself the prisoner of a Genii commander, along with a desperately hungry Wraith who has been separated from his hive.

As Dr. Rodney McKay and Dr. Daniel Jackson is held prisoner by the Vanir, they make a startling discovery about who they really are. Meanwhile, "Todd" and his Wraith hijack the Daedalus to find and destroy those who activated the Attero device. The Travelers arrive and Lt. Colonel John Sheppard must help them get to the planet before "Todd" uncovers a way to discover the device for good, even if it means sacrificing McKay and Jackson's lives to do so.

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.

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.

An unstoppable energy weapon leaves Atlantis under siege after Earth launches a preemptive attack against a very powerful enemy's homeworld.

Dr. Rodney McKay is infected with the Pegasus equivalent of Alzheimer's disease, known as Second Childhood, a common illness among the elderly in the galaxy. The only way to save him is a shrine on Talus. The downside is that it has turned into a Wraith outpost.

"Todd" informs the Atlantis expedition that a rogue group of Wraith has acquired several Zero Point Modules to power a Super-hive, and wants it destroyed. However, after the Daedalus is disabled, they learn that the ship is heading straight for Earth, and they must stop it before it gets there.

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.

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.

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 a massive storm threatens the city, Atlantis is evacuated -- only to be taken over by the team's newest enemy.

Rodney McKay is reunited with his estranged sister back on Earth, who has given up a brilliant career as a scientist to raise a family.

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.

Plagued by terrifying nightmares, Teyla begins to recall a time when she and her father were captured by the Wraith and subjected to disturbing experiments.

The team desperately attempts to stop two Wraith hive ships from reaching Earth. Sheppard must rely on an old foe to rescue McKay and Ronon.

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.

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.

The Atlantis expedition mysteriously finds the Daedalus, abandoned and drifting in space. When Lt. Colonel John Sheppard's team come to investigate, the ship mysteriously disappears. They soon discover that the ship is actually an alternate Daedalus from a Alternate reality, and the team must find a way back to their Universe or risk being stranded forever in an unfamiliar reality.

McKay's efforts to harness the energy of an alien planet's atmosphere allows for a return trip to Earth -- but the team may not be able to return to Atlantis.

All hope seems lost, until Colonel Everett arrives suddenly from Earth. He is determined to defend the city until the arrival of a ZPM, brought by a new ship.

A run-in with a Wraith Dart leaves the consciousness of a precocious Atlantis security officer trapped in Dr. McKay's mind.