A secret group of scientists have discovered the location of the famous lost city of Atlantis, but it's not on Earth. It's located in another galaxy altogether, the Pegasus galaxy. Stargate Atlantis, a spin-off from the highly successful Stargate SG-1 series, follows a multinational scientific and military group, lead by Diplomat Dr. Elizabeth Weir, headed on a one way trip to Atlantis. Their mission: to investigate the secrets of Atlantis, a city now known to have been built by ancient powerful beings, and bring whatever they discover back to Earth. They will be all on their own, with no means to return, with no means of rescue or support, unless they can find the technology they need in Atlantis to return them to Earth.  Once in Atlantis, the group finds the city abandoned; asleep for tens of thousands of years, and no power source left for a return home. They must find a power source within Atlantis' own Pegasus galaxy using the same stargate system that got them there or they will be stranded forever. On the first planet they visit, they accidentally waken a new, powerful, and more evil enemy than human kind has ever faced, the Wraith. And the Wraith are hungry – for humans!  Follow the extraordinary adventures of an SGA team lead by Major John Sheppard, and his team made up by his second in command Lt. Aiden Ford and the Astrophysicist/Scientist Dr. Rodney McKay, reprising the role he played in Stargate SG-1). Joining the team will be Teyla Emmagan, a beautiful, exotic, and strong-willed woman from the Pegasus galaxy.

In "Hide and Seek", Sheppard says that he doesn't really get into hockey. This is a reference to the main character in Stargate SG-1, Jack O'Neill, who loves hockey.

In "Rising", while in the "dining room" of the Female Wraith, clearly seen on the table is the head of a creature. This creature is a Mastage, which was seen in Stargate: The Movie.

The dog who appears as Elizabeth's dog in the episode "Home" is Torri Higinson's dog in real life.

Factual error: In the shot showing the team suiting up to make the first jump to Atlantis, there is a Russian member whose shoulder flag patch is sewn on upside-down, with the red stripe on top.

Continuity error: In "The Storm", there is a scene showing Jennai trainees dueling with quarterstaffs. Only three staffs are used, and they alternate between being plain wood or bearing a spiral stripe.