The twenty episodes that constitute the first season of Stargate: Atlantis introduced the audience to a new world, related to but separate from the world of Stargate SG-1. Finally, humans have discovered the legacy of the Ancients, the Lost City of Atlantis. As humans explore the city and encounter dangerous new enemies throughout the season, viewers are taken on a wild ride of adventure and drama, with just enough comic relief along the way.
While on the way back to Atlantis, a Puddle Jumper is stuck halfway through the Stargate. The team has thirty eight minutes before the Stargate shuts down, and the team will be blown into space. While another team works out a way to save them, a bug attaches itself to MajorJohn Sheppard's neck, and it is slowly killing him.
MajorJohn Sheppard's team's Puddle Jumper goes down on a routine mission due to electromagnetic interference. The team also make first contact with the inhabitants of M7G-677, who mostly comprise of children, since they believe that in order for the Wraith to leave them alone, they must kill themselves the night before their 25th birthday.
With their food supply running low, Teyla Emmagan suggests to the Atlantis expedition to make a deal with an Athosian trading partner, the Genii. However, the team discovers that they are not what they seemed, a militaristic civilization with a plan to destroy the Wraith.
A storm covering 20% of Lantea that strikes every 20 to 30 years is brewing and is heading straight for the mainland, and then Atlantis. As most of the expedition takes shelter on Manaria, a small group stays behind to work out how to save the city. Unfortunately, a Genii strike team, led by CommanderAcastus Kolya plan to seize Atlantis for the supplies the expedition promised them, and takes everyone prisoner.
While exploring sections of the city that was flooded during the storm, some of the scientists start dying after seeing realistic hallucinations that causes brain aneurysm. Their attempts to contain it doesn't go well, as one of the infected goes into a populated section of the city.
MajorJohn Sheppard's team are under attack from Wraith Darts, and then sees them wiped out through a mysterious energy beam. They search the planet below, Proculus, who do not have advanced technologies, but Dr.Rodney McKay suspects they are hiding something, especially after the priestess, Chaya Sar comes to Atlantis and has her eyes on Sheppard.
In the wake of discovering a fleet of three Hive Ships zeroing on Atlantis, Dr.Rodney McKay manages to give the Stargate enough power to dial Earth for one second, which is more than enough time to send compressed data, including the team members' messages to their families.
Teyla Emmagan is plagued with several nightmares about the Wraith. Soon, her team discovers that her ancestors were experimented on by a Wraith scientist, and she has Wraith DNA. This gives Teyla the capability to contact the Wraith from a certain distance, including those from the oncoming ships.
Earth, recently equipped with a Zero Point Module sends reinforcements to defend Atlantis until the new Earth ship, the Daedalus gets there. Soon, the ships arrive to seize the city, launching waves of Wraith Darts and beaming several soldiers down to the city.