Stargate Atlantis is set in the city of Atlantis, on a planet called "Lantea" in the Pegasus galaxy, built millions of years ago by the most advanced race 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 a planet in 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 into the ocean (in order to hide from the Wraith), which, in the Stargate universe, is the source of the Greek myth of the Lost City of Atlantis.
The city of Atlantis hosts much of the action in the series and is the source of much of the technology which the characters employ. While trying to uncover the secrets the city still holds from her new human inhabitants, the Atlantis expedition also use the Stargate to explore the Pegasus galaxy, looking for energy sources and other technology that the Ancients may have left behind and that may help them defeat the Wraith.
The events of Stargate Atlantis follow the cliffhanger Stargate SG-1 seventh season finale "Lost City", where SG-1 found an outpost made by the race known as the Ancients in Antarctica. After the events of Stargate SG-1 season eight premiere "New Order", the Stargate Command sends an international team to investigate the outpost. Soon, Dr. Jackson discovers the location of the greatest city created by the Ancients, Atlantis.
[edit] Season 1
Season 1 began airing in the United States on July 16, 2004. The Atlantis expedition, led by Dr. Weir, arrives to the city of the Ancients and quickly find themselves in a dire situation that forces them to seek new friends, the Athosians, but that also lands them with a powerful new enemy: the Wraith. Cut off from Earth, the expedition must survive in a new galaxy, while deciphering the Ancients' technology and finding a way to destroy the Wraith. Major Sheppard puts together a team consisting of himself, Dr. McKay, Lt. Ford and the Athosian leader Teyla, who serves as Atlantis first contact team. In one of their first missions, they make another enemy in the Genii, a human militaristic civilization with a 1950s level of technology. After they learn of several more revelations about the Wraith, Atlantis prepares to evacuate. But right before they can, a contingent from earth arrives with a way to help defend the city against the impending attack from the Wraith until their latest battleship can arrive. The season closes with a cliffhanger, as the Wraith continue their siege of the city.
[edit] Season 2
Season 2 began airing in the United States on July 15, 2005 and it picked up just where season 1 ended. The Atlantis expedition successfully avoids being culled by the Wraith by making them believe Atlantis has been destroyed, and recover semi-regular contact with Earth thanks to the Daedalus and the new ZPM. Sheppard is promoted to Lt. Colonel and former Runner Ronon Dex replaces Lt. Ford, now MIA.
The central plot of this second season is the development of Dr. Beckett's retrovirus, which can, theoretically, turn a Wraith into a human. While an incomplete version makes a young Wraith girl lose all her humanity and almost turns Sheppard into an Iratus bug, a more developed version is tested in a living Wraith, "Michael", with mixed results. Michael's wraith faction proposes an alliance with Atlantis, but they betray the team. The season closes again with a cliffhanger - The Wraith on their way to Earth.
[edit] Season 3
Season 3 premiered in the United States on July 14, 2006, picking up just where season 2 ended. Having stopped the Wraith from reaching Earth and having achieved another failure with the Wraith retrovirus, the expedition faces its third year in the Pegasus galaxy with the Wraith still a threat and a new powerful enemy bent on destroying the expedition and Atlantis: the Asurans. The situation becomes complicated when an experiment gone awry drains their only ZPM, leaving them without a power source for the city's shields. Soon thereafter, they find a lost Ancient vessel and subsequently lose the city of Atlantis when the crew of the Ancient ship reclaims it. The SGC sends General O'Neill and Richard Woolsey to try and negotiate an agreement between Earth and the Ancients to allow the expedition back in Atlantis. O'Neill and Woolsey dial Earth and inform them that the Asurans (self-replicating nanobots) are taking over the city. They kill off the Ancient crew who reclaimed the city after 10,000 years. The main members of the Atlantis expedition on Earth disobey the orders and go back to the city, rescue it, and destroy all the Asurans. The season finale starts off with Earth launching a first strike against the Asurans who are building an armada to attack Earth. The Asurans counterattack by attacking Atlantis by means of a powerful beam weapon fired through a satellite housing a Stargate. As the last resort, the Atlantis team fires up the city's stardrive and escapes into space. The finale ends when the hyperdrive malfunctions, leaving the city flying through uncharted space with a day's worth of energy left in their sole ZPM and Dr Weir critically injured.