| Stargate: Atlantis follows the present-day adventures of John Sheppard and his military team from Earth that, along with two dozen other teams, venture to distant planets. They use an alien device known as a Stargate, which is housed in the city of Atlantis on the planet "Lantea". The city was built millions of years ago by one of the most advanced races of the Stargate universe: the Ancients. Five to ten million years ago, due to a plague in the Milky Way Galaxy, they were forced to flee to the Pegasus Galaxy, and there they seeded life on hundreds of worlds as they had done in the Milky Way. After encountering a powerful enemy known as the Wraith and going to war with them for more than one hundred years, the Ancients ultimately lost and were forced to submerge their city beneath Lantea's ocean, which, in the Stargate universe, is the source of the Greek myth of the Lost City of Atlantis. Stargate: Atlantis episodes feature a self-contained story that also contributes to the larger storyline of the war against the Wraith and the Atlantis residents' search for the means to destroy their enemy. Each season has also featured a two-part episode, and a few episodes that, while not technically two-parters, feature direct continuity with the story of the previous episode (for example, season 3 "Progeny" and "The Real World"). Each episode begins with a cold open, sometimes preceded by a recap of events relevant to the upcoming narrative. The opening credits feature an original theme by Joel Goldsmith. Though they were drastically cut at the start of season 2, the full credits were recovered after the mid-season two-parter. They were again cut short in the 5th season.
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| John Sheppard: Joe Flanigan as John Sheppard (seasons 1–5 main): a United States Air Force Major recruited to the Atlantis Expedition due to his intuitive mastery over Ancient technology. He becomes the de facto commander of Atlantis' military contingent after the original mission commander Colonel Marshall Sumner is killed. His position is made official in season 2 after Atlantis re-establishes contact with Earth, and he is promoted to Lieutenant Colonel.
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| Rodney McKay: David Hewlett as Rodney McKay (seasons 1–5 main): a brilliant scientist who is a member of Sheppard's team and the head of the Science and Research Departments on Atlantis. One of the foremost experts on Ancient technology, he was first introduced as a professional rival of Samantha Carter in the fifth season of Stargate SG-1.
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| Teyla Emmagan: Rachel Luttrell as Teyla Emmagan (seasons 1–5 main): the leader of the Athosians, a race of humans native to the Pegasus galaxy. She befriends Sheppard when he visits her homeworld and joins his team in order to fight the Wraith. She has the ability to sense the presence of the Wraith.
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| Aiden Ford: Rainbow Sun Francks as Aiden Ford (season 1 main, seasons 2, 5 recurring): a young First Lieutenant in the US Marine Corps, who is a member of Sheppard's team in season 1. In season 2, he becomes mentally unstable due to an overdose of Wraith feeding enzyme, and abandons Atlantis.
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| Elizabeth Weir: Torri Higginson as Elizabeth Weir (seasons 1–3 main, seasons 4–5 recurring): a diplomat and expert in international politics, who leads the initial Atlantis Expedition after briefly serving as the head of Stargate Command in Stargate SG-1. She is a main character in seasons 1-3; in the season 3 finale she is critically wounded by a Replicator attack. She is a recurring character in season 4, having been captured by the Replicators.
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| Carson Beckett: Paul McGillion as Carson Beckett (seasons 2–3, 5 main, 4–5 recurring): the Chief of Medicine of Atlantis in seasons 1-3. In the season 3 episode "Sunday", he is killed in an explosion caused by Ancient technology. However, a clone of him created by the rogue Wraith "Michael" appears as a recurring character in seasons 4 and 5.
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| Ronon Dex: Jason Momoa as Ronon Dex (seasons 2–5 main): a weapons specialist from the Pegasus planet Sateda. After his world fell to the Wraith, he was turned into a "runner" and hunted relentlessly for seven years. He joins Sheppard's team on Atlantis after Dr. Beckett removes his Wraith tracking device.
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| Samantha Carter: Amanda Tapping as Samantha "Sam" Carter (season 4 main, 5 recurring): an astrophysicist and United States Air Force Lieutenant Colonel, who was a main character for the entire run of Stargate SG-1. In season 4, she is promoted to Colonel and given command of the Atlantis Expedition.
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| Jennifer Keller: Jewel Staite as Jennifer Keller (seasons 3,5–5 main): the Chief of Medicine on Atlantis, who replaces Dr. Beckett in the third season finale. She is listed as a main character after Carson Beckett's death.
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| Richard Woolsey: Robert Picardo as Richard Woolsey (season 5 main, seasons 3–4 recurring): a representative of the International Oversight Advisory, who first appeared as an agent of the NID in season 7 of Stargate SG-1. In season 5, he replaces Samantha Carter as commander of Atlantis.
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