Stargate Atlantis (usually stylized in all caps and often abbreviated SGA) is a military science fiction adventure television series and part of MGM's Stargate franchise. The show was created by Brad Wright and Robert C. Cooper as a spin-off series of Stargate SG-1, which was created by Wright and Jonathan Glassner and was itself based on the feature film Stargate (1994). All five seasons of Stargate Atlantis were broadcast by the Sci-Fi Channel in the United States and The Movie Network in Canada. The show premiered on July 16, 2004; its final episode aired on January 9, 2009. The series was filmed in and around Vancouver, British Columbia, Canada.

The story of Stargate Atlantis follows the events of Stargate SG-1's seventh season finale episode "Lost City" and eighth season premiere episode "New Order" in which the cast of that series discovered an Antarctic outpost created by the alien race known as the Ancients. In the pilot episode "Rising", Dr. Daniel Jackson discovers the location of Atlantis, the legendary city created by the Ancients, and Stargate Command sends an international team to investigate it.

The series was a ratings success for the Sci Fi Channel and was particularly popular in Europe and Australia. Although it received little critical response, Stargate Atlantis was honored with numerous awards and award nominations in its five-season run. With the cancellation of Stargate Universe, the intended direct-to-DVD Stargate Atlantis movie entitled Stargate: Extinction was cancelled.

Stargate Atlantis follows the present-day adventures of Major John Sheppard and his military team from Earth that along with two dozen other teams explore distant planets in the Pegasus Galaxy. They use an alien device known as a Stargate that was built millions of years ago by an advanced race of people known as the Ancients. The expedition is based in the Lost City of Atlantis on the planet "Lantea". The city was abandoned 10,000 years ago by the Ancients, who were forced to flee after losing a long war to a powerful enemy known as the Wraith. They 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 story line 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 some episodes feature direct continuity with the story of the previous episode. 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 cut at the start of season 2, the full credits were recovered after the mid-season two-part episode.

Season one began airing in the United States on July 16, 2004. The Atlantis expedition, led by Dr. Elizabeth Weir, arrives at Atlantis, the city of the Ancients. The expedition quickly finds itself in a dire situation that forces them to seek new friends, the Athosians, but they also acquire a powerful new enemy: the Wraith. Due to the power requirements for reaching Lantea, they are unable to contact Earth. The expedition must survive in a new galaxy, while deciphering the Ancients' technology in order to find a way to destroy the Wraith and to acquire important new knowledge. Major Sheppard puts together a team consisting of himself, Dr. Rodney McKay, Lt. Ford and the Athosian leader Teyla Emmagan, who serve as Atlantis' first contact team. In one of their first missions, they make another enemy, 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, 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 where Season 1 ended. The Atlantis expedition successfully avoids being culled by the Wraith by making them believe Atlantis had been destroyed, and they recover semi-regular contact with Earth, thanks to the starship Daedalus and power from a new Zero Point Module (ZPM) recovered by SG-1. Sheppard is promoted to Lt. Colonel and as Lt. Ford, who went missing in action (MIA) at the end of the battle with the Wraith, is replaced by Ronon Dex a human freed from the Wraith. 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 on 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 are heading for the rich feeding grounds of Earth.

Season three premiered in the United States on July 14, 2006, picking up where season 2 ended. Having stopped the Wraith from reaching Earth and having failed to develop a working 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, self-replicating nanobots, also known as Replicators. 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 unwillingly turn over the city of Atlantis to its crew. The SGC sends General O'Neill and Richard Woolsey to try to negotiate an agreement between Earth and the Ancients to allow the expedition to return to Atlantis. The Ancients are then subsequently killed by an invading Asuran force while O'Neill and Woolsey send off a distress call to Earth and go into hiding. The main members of the Atlantis expedition on Earth disobey their orders and go back to the city, rescue O'Neill and Woolsey, and repel the Asuran invasion. The season finale begins with Earth launching a first strike against the Asurans, who are building an armada to attack Earth. The Asurans counterattack by attacking Atlantis with a powerful beam weapon fired through a satellite housing a Stargate. As a 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.