The Ancients, a highly developed race credited with building the system of Stargates once inhabited an outpost in Antarctica. Millennia ago they departed from Earth. In the present day, the SGC has established a base in the outpost to learn more about the Ancients and the technology they left behind, which can only be operated by a small proportion of people possessing the ATA gene. The team is headed by Dr. Elizabeth Weir, also present are astrophysicist Dr. Rodney Mckay, Scottish medical Doctor Dr. Carson Beckett, British Scientist Peter Grodin and SG-1 team member Dr. Daniel Jackson. Daniel Jackson decodes a message that reveals to them an eight-symbol address which will take them to the Ancient's lost city - Atlantis, in the Pegasus Galaxy.
Brigadier General Jack O'Neill is making his way to the base in Antarctica aboard a helicopter piloted by Major John Sheppard who is stationed at the McMurdo Air Force Base and has no knowledge of the Stargate programme. When Dr. Beckett is enlisted as a guinea pig by Dr. Mckay to assist him in learning more about an Ancient chair found in the outpost, possessing the rare ATA gene, he accidentally activates a drone which almost brings down the helicopter as it approaches the outpost. Some evasive flying on the part of John Sheppard and the deactivation of the drone just in the nick of time see the General and Major arrive at the outpost unscathed. Daniel explains his amazing find to Jack who although reluctant at first eventually gives the mission to go to Atlantis a go. Elsewhere on the base Sheppard learns that he possesses the rare ATA gene when he activates the Ancient chair, only unlike Dr. Beckett he's a natural.
In the run up to the expedition’s departure date the team members bid their families farewell and Sheppard wrestles with the decision as to whether to go to Atlantis or remain on Earth - he chooses to go. The day of departure arrives and the gate room is filled with equipment, scientists and military personnel ready to embark on their journey to the Pegasus Galaxy. Colonel Marshall Sumner heads the military personnel, and is the first to step through the gate when a wormhole connection is established.
The members of the expedition all safely arrive in Atlantis and begin to explore the city. As they explore the city comes to life, with systems beginning to activate and light up. A bay filled with Ancient ships, a control room are found before they discover that the city is protected by an energy shield and is in fact underwater. Dr. Beckett discovers an Ancient hologram which tells the narrative of how the Ancients came to be in the Pegasus Galaxy. The Ancients left Earth and came to the Pegasus Galaxy, seeding human life on many worlds until they set foot on a dark world and found a terrible sleeping enemy - the Wraith. The enemy awoke and began feeding on those worlds populated by humans until only Atlantis remained. Thousands of years ago, the Ancients found themselves in a stalemate and decided to submerge the city and return to Earth.
The expedition soon, however, find that power levels are dropping in the city - their presence is draining the city of the power it needs to sustain the energy shield holding back the ocean. With not enough power to continue to power the shield, or to dial back home to Earth the team dial another planet in the Pegasus Galaxy in hope of finding a ZPM to power the shield or refuge for the expedition should the shield fail. Colonel Marshall Sumner leads the team, which includes Major John Sheppard and Lieutenant Aiden Ford.
They arrive on the planet Athos in the dark and encounter two young children playing, the Father of one, Halling, mistakes them for traders and takes them to meet with their leader. Here they meet Teyla Emmagen, leader of her people. Although initially cautious of the strangers Sheppard slowly overcomes her reluctance. In the morning, when the sun rises it reveals the ruins of a city nearby, which the Athosians don't visit for fear that it will bring the Wraith down on them. Despite Teyla's warnings Sumner leads a team to the ruins to investigate, while Teyla takes Sheppard to some caves with old drawings on that tells the story of the Wraith cullings.
Back at the gate Lieutenant Ford watches as the gate activates and three wraith "darts" fly through. Sumner's team return to the encampment preparing to defend it, while Teyla and Sheppard rush back from the caves.
