Originally broadcast on television from11 July 2008 to 9 January 2009.

Special features of these DVDs: widescreen presentation ; audio commentaries ; mission directive featurettes ; deleted scenes ; photo & design galleries ; Dolby Digital ; scene selection.

Joe Flanigan, David Hewlett, Rachel Luttrell, Jason Momoa, Amanda Tapping.

After the secret base of the Ancients, originators of the stargates which allow for interplanetary travel, is discovered, Stargate Command leads a multi-national group to travel to a distant galaxy and bring back new technology but ends up stranded there.

Search and rescue: After the explosion of Michael's medical compound, which caved in, trapping the Atlantis team and the marines, Colonel Samantha Carter sends a rescue party along with a medical team and the combat engineers, as well as a new addition to the Atlantis team, Captain Alicia Vega. As the rescue starts, it appears that the team has been split into the two surviving groups of Ronan and Lt. Colonel Sheppard, and McKay and Major Lorne. When McKay finds Michael's hard drive, it contains a lot of data about his operations. Suddenly, McKay realizes that, when the compound self destructed, it sent out a subspace message that alerted Michael of their presence. With the Daedalus now in orbit, Michael appears and they engage into combat. As the battle progresses, they realize that Teyla could be aboard and they decide to mount a rescue mission to retrieve her. When they're aboard, it appears that Teyla is nearing birth and they'll have no chance of retrieving her in time.

The seed: Dr. Carson Beckett is removed from stasis because he's the only one who can find the antidote to a mysterious virus that has incapacitated base personnel, beginning with Dr. Jennifer Keller.

Broken ties: Ronon is abducted by a Wraith who tries to brainwash him.

The Daedalus variations: An empty Daedalus is found orbiting the planet. The team goes to check it out and they are transported to an alternate universe.

Ghost in the machine: A group of beings stranded in sub-space seek help from Atlantis to return to normal space. But their outrageous claims and erratic behavior strains the trust of their benefactors and forces a painful solution.

The shrine: Rodney is infected with a deadly illness known as "second childhood" which diminishes his mind capabilities and makes him lose his memory gradually.

Whispers: Sheppard and Beckett battle zombie-like, Wraith-engineered mutants with a team of the best and brightest female SG members. They also happen to be gorgeous - the SG team, not the mutants.

The queen: Sheppard, McKay, Teyla, Ronan and Jennifer Keller travel to a rendezvous with Todd the Wraith. Keller believes she has found a vaccine of sorts to modify the Wraith at a genetic level that will render it unnecessary for them to feed on humans. She needs test subjects however and Todd agrees but indicates that they will have to seek the support of the Queen of an allied Wraith hive. Since his own Queen has been killed, it will be necessary for someone to impersonate her - and the only person able to get away with that would be Teyla. She agrees but once on board the allied ship, it's very clear that Todd hasn't been entirely forthcoming as to his exact plan.

Tracker: Jennifer, Ronon & Rodney find themselves in the middle of a Wraith fox hunt when Jennifer is kidnapped by a runner (the fox) to help him with an humanitarian mission.

First contact: Dr. Daniel Jackson comes to Atlantis in search of a lost Atlantian room. The discovery reveals a new race. Daniel and McKay are kidnapped by the new race and are forced to finish a device which may kill the Wraith. Todd feels betrayed and takes the Daedalus.

The lost tribe: The new race that stole the device, not to mention Rodney and Daniel, turns out to be an old one meaning very old and well known to the human race. With an ancient grudge to settle they force Rodney to activate the device against the Wraith with a side effect that could kill millions through out the galaxy. That make the Wraith mad so they abscond with the Daedalus to retaliate. Once again we lowly humans have to take control of a messy situation to keep the master races from wreaking havoc in the galaxy.

Outsiders: The Atlantis team endeavors to thwart Wraith plans to either find a cure for the retrovirus or exterminate all those infected.

Inquisition: Sheppard and his team are lured to a planet and are soon put on trial for crimes against the people of the Pegasus galaxy. In flashbacks, the three judge tribunal recounts the indictment against them including the re-awakening of the Wraith and the various missions where at least a few, if not more, innocent bystanders were killed. Sheppard does his best to argue that on balance, fewer were killed by their presence than would have been the case if they had never been there. A least one of the judges is clearly determined to find them guilty while a second seems far more sympathetic. It's left to Richard Woolsey, who has now joined them, to plead the rest of their case. A lawyer by profession, Richard clearly knows how the game is played and focuses on that third judge.

The prodigal: When the power is shut down and most of the inhabitants are locked out of key controls, it is apparent that Atlantis has been taken over by an off-world group, soon identified as Michael and his hybrids. He is after Teyla's newborn child who is key in his quest to gain control of the Pegasus galaxy. While Sheppard and McKay try to get their hands on a jumper to launch an attack, Ronan and others who were taken prisoner by Michael during his initial invasion launch reprisals of their own. When Teyla manages to get away and hide, Michael gives her a simple choice: surrender herself and her child to him or he will use the city's self-destruct mechanism to kill everyone.

Remnants: Radek discovers an alien device that Rodney finds holds serious surprises. Sheppard runs into a reincarnated Acastus Kolya who plans to attack Atlantis. An IOC representative arrives to replace Woosley who receives advice from a mysterious woman.

Brain storm: Rodney finally invites Jennifer on a date; to attend a science conference with him. But petty jealousies arise at the conference that have to be suppressed when a proposed solution for global warming has potentially lethal side effects.

Infection: A Wraith cruiser arrives at Atlantis and is strangely uncommunicative. The anti-wraith drug story arc is concluded and we see a relationship blossom.

Identity: An alien mind takes up residence in Jennifer's body and seems as confused as her colleagues are by her erratic behavior. Which begs the question; where is Jennifer?

Vegas: The killings a Wraith is making in Las Vegas are investigated by detective John Sheppard... who knows nothing about life-sucking aliens from another galaxy.

Enemy at the gate: A hive ship turbo-charged with a ZPM has received the Wraith's message from a alternate universe containing the location of Earth. The ship is now heading for Earth.

Not rated.

DVD.

Audio track in English, French and Spanish ; subtitled in English, Portuguese, and Spanish ; closed captioned for the hearing impaired.