After the gate address to the lost city of Atlantis is found, an expedition departs to the Pegasus Galaxy to check it out. Unfortunately, the city is found on the bottom of the ocean floor, and its shields are quickly losing power. In search of a ZPM or a safe place to stay, a team is sent to the planet Athos. They befriend the planet's inhabitants, but evil beings known as the Wraith then arrive.

The Wraith have captured many of the Athosians and SGA expedition members, before leaving through the Stargate. Back at Atlantis the shields continue to lose power, due to the limited energy left in the last remaining ZPM. Major Sheppard eventually gets approval to lead a rescue mission to the Wraitha 's shipa 's location. The rescue team finds almost all the Wraith are in hibernation in the ship and the captured people stored in cocoons or holding cells. Sheppard must find away to rescue the people, before more Wraith awaken, but he also is faced with making a terrible sacrifice along the way.

Kids playing a game of hide and seek in the city, accidentally release a strange and apparently malevolent energy force, which threatens all of Atlantis. Meanwhile, Dr. McKaya 's experiment with an Ancient personal protection device leads to a threat to his life. Can the Atlantis team defeat a formless energy alien while trying to also save Dr. McKay from a slow death?

After Sheppard is attacked by a strange, Wraith-like bug, the team heads back to Atlantis through the planet's orbital stargate. However, their Puddle Jumper gets stuck in the gate when the engine nacelles fail to fully retract into the Jumper, leaving them only thirty-eight minutes to get through the Stargate before the wormhole's event horizon closes.

The team comes in hot, having encountered the Wraith for the fifth time in nine missions. Therea 's no longer any doubt: someone in Atlantis spies for the Wraith. Weir convenes a planning meeting that excludes Teyla. She and Lieutenant Ford establish protective zones against sabotage that exclude the Athosians and interview the Athosians one by one. The Athosians become angry at this suggestion that theya 're not trusted. Weir and Sheppard must uncover the spy without alienating the allies who know the Pegasus galaxy.

Shortly after detecting an energy field, the team's Puddle Jumper unexpectedly crashes. As they begin searching for the field's source to shut it down in order to get their Puddle Jumper working again, they run into a village of children that believe that killing themselves when they reach the age of 24 keeps the Wraith away.

With Beckett's help, a planet's inhabitants create a drug capable of preventing the Wraith from feeding on them. However, they soon discover the devastating side effects it has on both the Wraith and the user.

The Atlantis team travel to the planet of the Genii, known by the Athosians to be good traders of food and crops. As Tayla and Ford barter for food with the farmers, Sheppard and McKay stumble on a secret underground research facility, which belies the societya 's technological backwardness. The Genii are close to developing atomic bombs to use against the Wraith. After being captured in the secret site, McKay is intrigued, while Sheppard remains skeptical. Now the team must either forge an alliance with these unlikely allies, or find a way to extricate them selves from being killed by the Genii, now that they know the team knows their secret.

After McKay discovers that a mist covering an alien planet can be used as a powerful energy source for the Stargate, the expedition is able to dial back to the SGC. Told that the Prometheus is being outfitted with Asgard hyperdrives capable of quickly returning them to the Pegasus Galaxy, members of the expedition return to Earth. However, their hopes of returning to Atlantis are shattered when they are informed that due to an accident aboard the Prometheus, they can't go back. Now separated from Atlantis and stuck on Earth, the team finds strange changes in the things they see and encounter there; the friends and people they knew at the SGC are acting differently than expected. Sheppard begins to suspect what is really going on, but how can he determine if he is correct?

A devastating storm occurring every twenty or thirty years is detected approaching Atlantis. The city is evacuated while McKay, Weir, and Sheppard initiate a plan to use the storm's lightning to power the shields. However, before they can finish, they are interrupted by the Genii, who plan to take over Atlantis.

With Weir and McKay held hostage by the Genii, Sheppard must figure out how to both rescue them and save Atlantis before the storm hits.

After locating an Ancient defense satellite, Sheppard, McKay, and two scientists detect a Wraith distress signal coming from a nearby planet. They investigate but soon become trapped when an unstoppable Wraith prevents them from reaching their Puddle Jumper.

When members of the expedition begin falling victim to a contagious nanite virus capable of causing death within hours, Atlantis goes into an automatic lockdown. [Read Recap below]

When Sheppard and his team are fleeing from the Wraith in a planet's orbit, an energy wave suddenly wipes the enemy out. Thinking the planet has a powerful weapon, the team investigates, finding a civilization untouched by the Wraith and living in perfect health. They then meet Chaya Sar, the planet's High Priestess, who tells them that it wasn't a weapon, but the work of the goddess Athar.

During a search of the city, the team finds a 10,000 year-old woman in suspended animation. Thinking she is an Ancient, they wake her up. However, she then reveals that she is Elizabeth Weir. [Read Recap below]

The team heads to one of the planets on the list of Ancient outposts, and with the help of the planet's inhabitants, they search for the ZPM. However, old foes show up and plan on taking the ZPM for themselves. [Read Recap below]

McKay figures out how to send a message back to the SGC, prompting the expedition members to film messages for their families.

Teyla begins to have vivid nightmares about the Wraith. Soon this starts affecting her duties. She becomes easily distracted, causing Sheppard to order her to see Dr. Heitmeyer. The session leads Teyla to consult an Athosian elder about her past. The information the elder gives her leads the team to investigate a strange planet where Teyla and her father once lived. What they find there, and what Dr. Beckett subsequently finds out about Tayla through blood tests, shocks the small group, who learn of Teylaa 's secret.

With a group of Wraith hive ships on the way to Atlantis, the team searches for a place to flee and a way to destroy the city. McKay leads a team to try and activate the Ancients' orbital weapons platform.

A new military contingent from Earth is sent to take command of Atlantis and defend it from the impending Wraith attack.