The discovery of an outpost, left behind by the Ancients in the most unlikely of places, leads a new Stargate team to the distant Pegasus galaxy. Once there, they discover a planet of humans being decimated by a terrible alien race know as the Wraith.
Sheppard tries to convince Weir to mount a rescue mission to free Colonel Sumner, Teyla and the others captured by the Wraith. Meanwhile, Sumner faces the Wraith themselves.
An alien intruder has found its way into the city, threatening the security of the base. Dr. McKay's experiments with alien technology land him in trouble.
The Puddle Jumper has been damaged and is stuck part way through an Orbital Space Gate. The team have only 38 minutes to find a way to dislodge themselves before the Stargate shuts down, cutting the Jumper in half. To make matters worse, John Sheppard has an alien creature attached to his neck that is sucking the life from him.
After another dangerous encounter with the Wraith, the Earth team begins to suspect they have a traitor in their midst. Suspicion falls on the Athosians, and Teyla finds herself caught in the middle.
The team crash lands on a planet where the locals, in fear of the Wraith, practice ritual suicide when they reach the age of twenty-five.
The team investigates a drug being developed on another world that has the potential to repel the Wraith's feeding on humans.
Gating to the planet Genii to trade for food, the team discovers what appears to be a simple, farming population. But they are preparing a deadly weapon to attack the Wraith, and when Sheppard and McKay are interrogated it appears the Genii may not make the best of allies.
The Atlantis team plans to use a planet's unique atmospheric fog to acquire the power they need to gate back to Earth.
The inhabitants of the city and the mainland are forced to evacuate when a huge hurricane bears down on them. But things get even worse when the city is then captured by the Genii, forcing Sheppard to try and stay one step ahead when they capture Weir and McKay.
Sheppard attempts to rescue Weir and McKay and retake the city. Meanwhile Beckett, Teyla, and Ford try to navigate the storm and lend assistance.
Sheppard's team investigates a downed Wraith ship, and find themselves stuck on a planet dealing with a lone Wraith survivor.
Several residents of Atlantis are infected with a deadly nanite virus, forcing a lockdown of the entire city.
The Atlantis team encounters a pre-technological world strangely untouched by the Wraith. They hope to negotiate with the local population to provide a home for the refugees of Wraith attacks, currently living in Atlantis.
A very old 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.
The planet Dagan may be home to a vitally important ZPM, capable of restoring Atlantis' shield and protecting the city from the Wraith, but a mysterious 'Brotherhood' on the planet - and their knowledge of the Genii - suggest that the planet may not be what it seems.
With a brief opportunity to send a data transmission to Earth, members of the Atlantis expedition compose video messages home to their loved ones. Meanwhile, Sheppard and Teyla use the Stargate to take a Jumper to do some reconnaissance on the approaching Wraith fleet.
Plagued by terrifying nightmares, Teyla investigates and discovers with the help of an older friend that she is a descendant of humans who were subjected to genetic experiments by the Wraith.
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.
A new military contingent from Earth is sent through the Stargate to take command of Atlantis and defend it from the impending Wraith attack.