1.01 "Rising Part 1"
- When SG-1 discovers what they believe to be the remnants of the Lost City of the Ancients — the originators of the Stargates — Stargate Command launches an investigation. A new team of explorers, headed by civilian Dr. Elizabeth Weir, travels to the distant Pegasus Galaxy, where they discover an advanced but deserted city on the ocean floor, a group of nomadic humans, and a deadly enemy that feeds on humans as an energy source!
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1.02 "Rising Part 2"
- Maj. John Sheppard assumes command after the expedition's commanding officer, Col. Marshall Sumner, is captured by the Wraith. While the city of Atlantis rises from the bottom of the ocean, Sheppard must perform a deadly deed that will haunt him for the rest of his life.
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1.03 "Hide And Seek"
- During a game of hide-and-seek, one of the Athosian children inadvertently releases a dark entity. And when Atlantis goes through a series of technical malfunctions, the team realizes that the shadowy creature is actually feeding off of the power supply!
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1.04 "Thirty-Eight Minutes"
- Fleeing from a surprise encounter with the Wraith, the Atlantis team's puddle jumper speeds back towards the Stargate, but becomes trapped when the puddle jumper suffers a mechanical failure. They have only thirty-eight minutes before the Stargate shuts down...and with the front half of the ship already de-materialized in the event horizon, the puddle jumper will be cut in half!
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1.05 "Suspicion"
- When the Atlantis team is ambushed by the Wraith on an off-world trip, Dr. Weir begins to suspect that one of the Athosians is actually a Wraith spy. Despite the disapproval of Teyla and Sheppard, she confines the Athosians to the south side of Atlantis and interviews them. But when the interviews take on an accusatory tone, growing tensions cause a mass exodus of Athosians from the city.
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1.06 "Childhood's End"
- The team discovers a primitive, forest-dwelling tribe that has been untouched by the Wraith for centuries. Unaware of the electromagnetic field that protects them from the Wraith's technology, the tribe believes that ritual suicide at the age of twenty-five keeps the Wraith at bay.
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1.07 "Poisoning The Well"
- Exploring a new 'gate address, the team encounters the Hoffans, a human civilization that has developed a drug with the potential to make them immune to the Wraith. When they learn of the Wraith's awakening at the hands of the Atlantis team, the Hoffan leaders grow impatient and demand that their people be inoculated before the drug is proven safe.
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1.08 "Underground"
- When Atlantis' rations begin to dwindle, Dr. Weir concentrates on trading with other worlds for food. Sheppard, McKay, Ford, and Teyla undertake a trading mission with the Genii, a simple farming people. But beneath their crops, the Genii hide both a secret defense system...and their desire for war!
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1.09 "Home"
- When Dr. McKay discovers a way to open a wormhole back to Earth, the team is overjoyed to learn that they can return to Atlantis within a month. But when the hyperdrive of the ship Prometheus is accidently destroyed, so too are their hopes of returning to Atlantis.
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1.10 "The Storm Part 1"
- With a monstrous storm that occurs only once every 20 or 30 years bearing down on Atlantis, Sheppard requests temporary refuge for the Atlantians on Manara. Meanwhile, McKay and Zelenka hatch a plan to use the electricity from the storm to raise Atlantis' protective force field.
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1.11 "The Eye Part 2"
- With Atlantis under the control of the Genii and the team scattered, Sheppard must play a dangerous game of cat and mouse with the soldiers to save the remaining members of the Stargate team, as the city faces imminent destruction.
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1.12 "The Defiant One"
- Investigating an Ancient weapons platform in space, Sheppard and McKay discover the wreckage of a downed Wraith ship on a nearby planet. On the planet's surface, they learn that it is a supply ship, transporting humans for food. What they don't know is that a single Wraith has survived the crash — and has stayed alive by feeding off the cargo!
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1.13 "Hot Zone"
- When members of the team show signs of an unusual infection, it is discovered to be caused by a nanite virus, which induces hallucinations and then death due to brain hemorrhage. Can the deadly technology be stopped before it cuts down the entire city?
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1.14 "Sanctuary"
- The Atlantis team visits a pre-technological paradise and requests that they be allowed to bring refugees of Wraith attacks there for sanctuary. The locals refuse, believing that the goddess Athar has restricted their planet from colonization by outsiders. But when Sheppard invites Athar's priestess back to Atlantis, is he inviting trouble into their midst?
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1.15 "Before I Sleep"
- The Atlantis team discovers a stasis chamber holding a woman who appears to be over 10,000 years old. Excited at the possibility that she is one of the alien race that built Atlantis, the team decides to bring her out of stasis despite the risks to her health. But everyone is shocked when, once reanimated, the elderly woman identifies herself as none other than Dr. Weir!
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1.16 "The Brotherhood"
- The Atlantis team travels to Dagan, a planet populated by a people whose ancestors once worshipped a ZPM as a religious symbol. But even as the team searches for keys to its whereabouts, the Genii have learned of their activities on Dagan and planted a sleeper agent amongst them. Now, with the Atlantis team closing in on the location of the ZPM, the Genii close in on them!
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1.17 "Letters From Pegasus"
- Having learned that the entire Wraith armada is headed towards the city, the team decides to use their remaining power to send Stargate Command a message containing information about the Wraith threat and the well-being of everyone on Atlantis. As most of the team are recording messages to their loves ones, Sheppard and Teyla embark on a mission that takes them directly to the Wraith army!
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1.18 "The Gift"
- When terrifying nightmares about the Wraith haunt Teyla, she visits the city's psychologist and learns that she can sense the Wraith. Determined to discover more, she leads a small team on a mission to a planet from which victims of the Wraith "miraculously" return. There, they uncover what appears to be a genetics laboratory. Could Teyla's connection to the Wraith be the result of genetic experimentation?
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1.19 "The Siege Part 1"
- With the Wraith armada closing in on Atlantis, tension builds between Teyla and some of the other members of the team over her connection to the Wraith. When she is accused of revealing the team's location after a scouting mission ends in a firefight, Sheppard steps in to defend her. But even he begins to harbor doubts when her accuser is left unconscious after an attack by an unknown assailant.
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1.20 "The Siege Part 2"
- As the Wraith attack on Atlantis begins, the team is bolstered by the appearance of reinforcements from Earth armed with nuclear warheads and good news: The battleship Daedalus is due to arrive in four days. But when the warheads are easily destroyed by the Wraith, it becomes increasingly clear that the reinforcements aren't enough to protect the city for four hours, let alone four days!
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