Several million years ago, in a beautiful alien city in Antarctica, a man and a woman in silver clothing - two of the Ancients who created the Stargates - look out a window sadly as the city rises out of the encroaching ice and flies away to the stars, leaving behind only a small outpost.
Present day: At the Ancients' abandoned outpost (discovered in the Stargate SG-1 episode "Lost City," Part 2), Dr. Elizabeth Weir, head of the Stargate Atlantis project, rides an elevator with Lt. Aiden Ford down a deep shaft bored in the ice. Reaching the research facility below, they find Dr. Rodney McKay and Dr. Carson Beckett arguing over the fact that Beckett is afraid to sit in the Ancient chair that controls the most powerful weapons known to humankind - even though he possesses (and is the one who discovered) the mutant gene to which Ancient technology automatically responds. As Weir points out, only a handful of people have the gene, and every time one of them sits in the chair they learn more about the Ancients.
Dr. Daniel Jackson of Stargate Command then tells Weir and McKay of a remarkable discovery he has just made: The stargate address to the lost city of Atlantis is incomplete. On a white board he adds an eighth symbol - indicating that Atlantis is not on Earth nor even in the Milky Way galaxy, but on a planet far, far away. And they can 'gate there.
As Gen. Jack O'Neill races to the outpost in a helicopter flown by Maj. John Sheppard, McKay convinces Beckett to sit in the chair. It activates and launches an Ancient drone weapon that almost destroys the helicopter. Thanks to Sheppard's fancy flying and Beckett's newfound ability to turn off his control, the chopper lands safely.
At the outpost, Daniel tells O'Neill that the Ancients flew their entire city to a dwarf galaxy called Pegasus. In order for an expedition to 'gate that far, they need to boost the stargate with the Earth's sole ZPM (zero-point module), an Ancient energy source that currently is powering the outpost's defenses and is vital to Earth's defense against an alien attack. The 'gating might totally drain the ZPM.
And even if it doesn't, there won't be enough power for the Atlantis team to 'gate back.
O'Neill says no, but Daniel convinces him that by visiting the Ancients' city they might be able to find more ZPMs - and who knows what else - to protect Earth. The expedition's a go, though O'Neill insists Daniel is too valuable here on Earth to join them. Weir is placed in charge, with Colonel Marshall Sumner as her military commander. After some reluctance, Sheppard - who, it has been discovered, has the most potent variable of the Ancient gene - joins the offworld expedition along with McKay, Beckett, a military compliment and a full crew of the best and the brightest, representing more than a dozen countries.
They arrive in the city of the Ancients, which is chockablock with amazing technology, including its own gate room and a bay of spaceships. The city's power systems turn on as the Atlantis team explores it. Then, amazingly, they discover that the city - which they can now comfortably call Atlantis - is underwater, with a force field holding back the ocean. They also find a holographic message that tells them how the Ancients developed the stargates as a means of spreading life through the universe. They seeded countless worlds in this Pegasus galaxy, until discovering a planet with a warrior race that fed upon the defenseless human worlds until only Atlantis remained. Before it was too late, they submerged the city for protection.
Suddenly, McKay screams to turn off the hologram: The city's power is rapidly draining due to all the systems being automatically turned on - and the force field holding back the ocean is weakening quickly. Gating back to Earth is impossible without another fully charged ZPM, and the city's last module is almost depleted. However, 'gating to another world within the Pegasus galaxy is still an option. Weir has Sumner and Sheppard lead a team to recon a randomly chosen planet for the evacuation of the Atlantis team.
The planet, Athos, is populated by a race of pre-industrial humans living in fear of the Wraith, the warrior race of which the hologram spoke. The Athosian leader, a beautiful woman named Teyla, doesn't take kindly to Sumner's no-nonsense attitude, but warms up to Sheppard. As the military team investigates the nearby abandoned city of Teyla's ancestors, looking for refuge and ZPMs, Teyla takes Sheppard to a cave. The walls are covered with drawings telling the history of her people and how the Wraith wait a few hundred years for the population to replenish its numbers before attacking and "harvesting" them. She believes that the Wraith can sense when anyone goes into the city.
Sure enough, three dart-like ships fly through the stargate. The Wraith have returned.
The Wraith Darts begin firing and it seems like the Wraith have the Atlantis team surrounded on the ground. But Teyla informs Sheppard that the ships are projecting shadowlike illusions. Sheppard relays the intel to Sumner, who instructs his men to take out the ships with small-arms and bazooka fire. One ship is destroyed. Then Sumner, one of his men and some of the tribespeople, including Teyla, are beamed up to a Wraith Dart. The two remaining Darts escape back through the stargate.
At Atlantis, the force field is deteriorating, and parts of the city are being destroyed. McKay pressures Weir not to wait for the offworld team any longer. She gives the order to evacuate to Athos when, suddenly, the stargate activates - and from it emerges Sheppard, the remaining members of the offworld team and about 50 of the surviving Athosians.
With the city about to be crushed by the sea, Weir gives Sheppard hell for bringing in outsiders when Atlantis must be immediately evacuated. Her tirade is interrupted when the entire city shakes thunderously. This is it - the end....
Or is it? Atlantis rises through the ocean, breaking through the surface into the light of day.