Several million years ago, the Ancients are about to leave Earth in their great city-ship of Atlantis. Ayiana must remain behind for unknown reasons, and watches the great city slowly rise and disappear in the sky.
In Antarctica, millions of years later in 2004, a group of researchers and scientists are working in an underground laboratory. They are examining Ancient Technology, which includes an ancient drone, and a control chair. Dr. Carson Beckett is attempting to activate the chair, as he has the ATA gene, a special gene sequence that allows him to interface with Ancient Technology. However, Beckett is unwilling to sit in the chair, despite being the one to discover the secrets of ATA.

Dr. Weir, the leader of the proposed expedition to Atlantis, says that they need as many people they have with ATA to sit in the chair, so that they can learn more about its operation, however most people are afraid of it because it controls powerful weapons. As they are discussing the chair, Dr. Daniel Jackson interrupts and asks them to come with him.

Jackson discovers that Atlantis is an 8 symbol address

He has new news on the address where the Ancients went after they left Earth. They recently discovered a seventh symbol, the point of origin earth, but found that their address was incomplete. There was an eight symbol. Atlantis may be far, but it’s not out of reach. It is possible to go there.

At the same time, General Jack O’Neill and Major John Sheppard are flying in a chopper towards the base, discussing their opinions on the Antarctic Continent. At the Base, Dr. McKay wants Dr. Beckett to sit in the chair one more time. Despite objections, Dr. McKay gets Beckett to sit down, and asks him to try and imagine an image of their location in the Solar System. The chair activates, but it also activates one of the drones that the research team is studying. The drone heads up and out of the base, and targets O’Neill’s helicopter. Before they get the warning from the Atlantis base, though, the drone enters their visual range. Major Sheppard and O’Neill start to dodge the drone, while Weir tells Beckett to concentrate turning off the drone before it hurts someone. He manages to do so, moments before the drone impacts the chopper.

A rogue drone launches

Sheppard and O’Neill arrive at the base about seven minutes later. O’Neill leaves Sheppard with orders not to touch anything, while he goes to talk with Jackson, Weir, and McKay. Jackson tells everyone about how the Ancients left in their flying city a few million years ago, to settle in the Pegasus Galaxy. McKay wonders if it may be possible that they are still there, and Jackson cites that that itself is reason enough to go. O’Neill doesn’t mind, but there is one problem. They need the nearly depleted Zero Point Module to power the gate, but O’Neill doesn’t allow them to use it. However, the rest insist on using the ZPM, and they are fully aware of the mission’s one-way nature.

At the same time, Sheppard runs into Dr. Beckett, who was recounting the events of the drone. Sheppard blames him for “firing that thing,” but quickly forgives Beckett. Beckett then goes on to explain the ATA gene to Sheppard. In the process, Sheppard sits on the chair, regarding that the odds are against him having the gene. However, the chair lights up immediately, and Dr. Beckett rushes to get Dr. Weir. McKay asks Sheppard to do the same excercise of thinking about their location in the Solar System, and a map immediately appears above the chair. Because of his ability to use Ancient technology so easily, Weir asks Sheppard to join the team, and after a discussion with O’Neill, he accepts.

A bit later, all the members of the team are saying farewell to their loved ones. Some are able to disclose certain details about the mission, like Weir, but others have to fabricate stories.

A successful wormhole receives the applause of the Atlantis Expedition

At Stargate Command, the members of the expedition are preparing their supplies for departure. At the same time, Dr. McKay is tying in the ZPM to the Stargate power systems. While they wrap up, Dr. Weir makes a speech to everyone. If they achieve a wormhole, they go, and she offers them one last chance to withdraw their participation. No one withdraws, and they dial the gate. As the eighth chevron locks, a stable wormhole does indeed form, to the applause of the expedition team. The probe is sent through, and a viable atmosphere is detected. A military team is sent through first, and then the rest of the expedition. As soon as everyone is through, a bottle of champagne comes through the Atlantis gate and then it deactivates.

The Expedition arrives in Atlantis.

As they explore the compound, lights and systems start to come online. Security teams are exploring the city, but have found no signs of aliens, Ancients or otherwise. However, the teams discover a conference room, and a hanger of space ships. At the same time, McKay discovers the control room, and the Atlantean DHD. As they are powering up main systems, Colonel Sumner calls Dr. Weir down three levels, where they see through a window a huge, submerged city. It is Atlantis.

Lucky for them, a force field is holding back the water to prevent the collapse of the city. Dr. Beckett also found a holographic recording by an Ancient, telling the history of Atlantis. About 10,000 years previously, a powerful enemy besieged Atlantis, which is why they sunk their city, and went through the Stargate back to Earth. The entire story of Atlantis is true, only that one of the Ancient Greeks would have probably have heard it by an Ancient. However, a problem has arisen.

The power levels in the city are dropping, and as soon as the last of three ZPM’s fail, the entire city will become flooded. They compress the teams to smaller locations, and attempt to cut back on power. However, they will need to find more ZPMs if they want to survive, as their Naquadah generators cannot provide enough power on their own.

Colonel Sumner puts together an expedition team, which includes Sheppard, and they open the gate to the planet Athos. The first people they encounter are two Athosian children, Jinto and Wex, who are playing a game. At first perceiving them as a threat, the team later encounters Halling, who clears up the confusion, and takes them to Teyla, leader of the tribe. On their way, one of the children briefly tells Sheppard about a creature called a Wraith, and his ignorance of their species surprises both children.

Teyla Emmagan introduces herself, and Sumner introduces his team. She states that the Athosians do not trade with strangers, so Sheppard proposes that they get to know each other. He is quick to “break the ice,” and Teyla invites them to share a cup of stout tea.

The next day, Colonel Sumner explains their proposition, but the Athosians fear that they may provoke the Wraith by entering the great city (a settlement across the lake). When Sumner shows ignorance of the Wraith, the first thing Teyla suggests is that they return to their world, as it best the Wraith never learn of their existence. Despite the warning, Sumner wants to explore the city, as there may be a ZPM there that the Athosians don’t know or care about. However, Sheppard is afraid that these Wraith may be the great enemy spoken about in the Ancient history. Teyla feels that it important Sheppard sees something, especially since they cannot return to their homeworld.

Back on Atlantis, the shield is in degragating condition, as another section of the city becomes flooded.

Teyla has taken Sheppard to some ancient ruins. There, Sheppard finds a necklace, which Teyla claims to have lost years ago. After putting it around her neck, Teyla begins to explain the Wraith history. They apparently sleep for periods of several hundred years, allowing the number of the humans to increase. They then return to cull them. Apparently, there are no species untouched by the Wraith. Also, there are some Athosians, like Teyla, who can sense the coming of the Wraith, which gives warning to the people.

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