Stargate Atlantis follows the adventures of a human expedition to the lost city of Atlantis in the Pegasus Galaxy. The Stargate has brought humanity into contact with other cultures, including new and powerful enemies: the Wraith, the Genii, and later the Asurans, all while trying to uncover the secrets the Ancients left behind.

Stargate Atlantis premiered on the US Sci Fi Channel on July 16, 2004 with "Rising", a movie-style two-part episode, that guest starred Richard Dean Anderson and Michael Shanks from Stargate SG-1. The series is broadcast in HD in selected countries including the US, which is shown sometimes on Universal HD and as of 2007 is now simulcast in HD on Sci Fi.

On August 20, 2008, it was announced that the series would end after 100 episodes and five seasons. At least one two-hour movie will follow.

Season 1-3

Season one began airing in the United States on July 16, 2004. The Atlantis expedition, led by Dr. Weir, arrives at 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 serve 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 several more revelations about the Wraith are made the expedition prepares to evacuate. Just before they do, however, a military contingent from Earth arrives to help defend the city against the impending Wraith attack long enough for Earth's latest battleship to arrive. The season ends with a cliffhanger, while the city is still under siege by the Wraith.

Season two 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 they 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 missing in action (MIA). The central plot of the 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.

Season three 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 to 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, also known as Replicators) 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 O'Neill and Woolsey, and cleverly repel the Asuran invasion. 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.

Season 4-5

Season four premiered in the USA on September 28, 2007, and in the UK on October 9, 2007. The writers stated that season 4 would take the series in a new direction. The future appears bleak with the incapacitation of Weir and multiple injuries among the senior members of the expedition. With the city damaged, running out of power and drifting in space, cut off from Earth, the Atlantis expedition raids Asuras to obtain a ZPM and is able to travel to a nearby planet. Weir is captured by the Asurans and Colonel Samantha Carter joins as a regular and acts as the expedition leader. She appeared in the episode "Lifeline" after helping to find and land Atlantis on its new home planet; however, it is stated that she has been ordered back to the SGC at this point. In episode 3, however, under the IOA's orders, Carter returns to Atlantis as the new leader of the expedition after Atlantis lands. The season focuses on the main antagonists; the Asurans and the Wraith, as well as the pregnancy of Teyla Emmagan. The Asuran base code is reprogrammed by McKay to start a war with the Wraith. Midway through the season, they are seemingly destroyed, and the remaining episodes concentrate mainly on Michael's efforts against both humans and the other Wraith.

In the fifth season, Richard Woolsey replaces Carter as the leader of the expedition. Teyla, who was held captive by Michael, gives birth to Torren John and escapes with her team, before they are able to cripple Michael. Eventually, he invades Atlantis with a commandeered Puddle Jumper to take Torren and destroy Atlantis, but thanks to the efforts of Sheppard and McKay, Michael is finally killed. The season also introduces a group of rogue Asgard, who unlike their Ida counterparts, actually experiment on Humans to prelong their lives, and steal an Attero device to destroy the Wraith, though the side effect is that any active Stargate would be destroyed. The device is eventually destroyed. With the Attero device, Michael and the Hoffan drug, the Wraith have become weakened, and is no longer the power of the galaxy they once were; the falling gives the humans freedom enough to establish a coalition. McKay falls in love with Keller, who eventually reciprocates his feelings, and are romantically involved. In the finale, "Todd" warns Atlantis that an upgraded Hive Ship is heading straight to Earth. Thanks to the efforts of the expedition, the ship is finally destroyed over Earth, and Atlantis lands near the coast of San Francisco.