يتكون الموسم الأول من ستارغيت أطلانتس من عشرون حلقة تعرف المشاهد بعالم جديد، متعلق لكنه منفصل عن عالم ستارغيت إس جي 1. أخيرا يكتشف البشر تراث القدماء، مدينة أطلانتس الضائعة. حيث يستكشفون المدينة و يواجهون مخاطر أعداء جدد في هذا الموسم، فيأخذون المشاهدين معهم إلى رحلة مغامرات و دراما.
A team led by Marshall Sumner, and some of the Athosians are kidnapped by a newly awakened enemy, the Wraith. Back in Atlantis, the city's shields fail, and the city rises from the bottom of the ocean. John Sheppard plans to rescue the missing team, but he may not reach them in time.
While the Atlantis expedition explore the city and make themselves at home for the long haul, Rodney McKay uses a shield emitter that can't be turned off, and a strange entity is accidentally unleashed on the city, and it's want for energy means grave danger for the Expedition.
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 sucked into space. While another team works out a way to save them, a bug attaches itself to John Sheppard's neck, and it is slowly killing him.
The First Atlantis Reconnaissance 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 Acastus Kolya plan to seize Atlantis for the supplies the expedition promised them, and takes everyone prisoner.
While exploring the Lantean system, John Sheppard and his team find a Wraith supply ship that crash landed on another planet for 10,000 years. While investigating it, the team discover that they are not alone, as the lone Wraith survivor who lived for 10,000 years by feeding on fellow Wraith awaken.
بعد إكتشاف أسطول من سفن هايف متجهة إلى أطلانتس، يتمكن رودني مكاي من إعطاء البوابة طاقة كافية للاتصال بالأرض لمدة ثانية، الذي يمكن خلالها بعث رسائل مظغوطة للأرض منها رسائل خاصة من أعضاء البعثة عائلاتهم.
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 Darts and beaming several soldiers down to the city.