First Season -- 2004
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Episode
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Summary
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Rising, pt 1
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At the Ancient outpost on Earth, Dr. Daniel Jackson figures out that they've been looking in the wrong galaxy for Atlantis. Now with a viable address, Dr. Elizabeth Weir puts together an expedition and heads through the stargate, knowing that if there isn't a working ZPM on the other side they won't be able to go home again.When they arrive, they discover that Atlantis is underwater -- and rapidly losing power to its shields.
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Rising, pt 2
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In an effort to find a world they can evacuate to, an Atlantis team discovers Athos and the Athosians, just in time for a Wraith raid (which they may well have triggered). Some of the team are captured, and after bringing the surviving Athosians back to Atlantis as refugees, Sheppard sets up a rescue mission. For the most part, the mission succeeds, but the end result is that the hibernating masses of Wraith are awakened. Major Sheppard winds up the ranking officer on Atlantis, which itself has broken free from the bottom and is resting on the surface with no shields to protect it anymore.
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Hide and Seek
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McKay volunteers to the first human trial for the ATA gene therapy, but once the new gene takes hold he finds himself stuck inside a personal shield that won't allow anything through -- including food and water. Meanwhile, an energy being that had been trapped in a containment vessel for millennia gets loose and starts wandering the city, eating any energy source it can find. In the end, McKay saves the city by walking into the entity's energy field and sending the naquadah generator that it's eating through the open wormhole, so that the entity follows it through to a barren world.
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Thirty-Eight Minutes
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With Sheppard dying from a large insect lodged in his throat and sucking the life out of him even as it steadily paralyzed him, the puddlejumper gets stuck halfway through an active stargate. If McKay can't come up with a way to retract the extended drive pods from inside the ship, with the help of the scientists back on Atlantis, they'll all die when the wormhole collapses thirty-eight minutes after it was established.
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Suspicion
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When Wraith show up on a few too many of the team's missions, Weir decides there must be a spy on Atlantis -- and assumes it must be an Athosian. Fed up with being under surveillance and generally treated like they were under house arrest, the Athosians decide to move to the newly discovered mainland to live, exploring it and raising crops for the benefit of everyone on the planet. Eventually it's discovered that Teyla's locket is basically a homing beacon for the Wraith, and they set a trap using it as bait -- and capture a live Wraith.
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Childhood's End
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Sheppard's team crash lands in their puddlejumper on a world populated entirely by children and very young adults, most of whom don't trust the presence of ' full-growns' . McKay's decision to remove and study the ZPM powering their defensive shield leaves the world open to Wraith attack, putting everyone in danger.
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Poisoning the Well
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The team and Beckett get involved with the Hoffans, who are developing a drug that will make them immune to the Wraith's feeding practices. But the two groups begin to clash when the Hoffans want to rush into human trials and mass production, rather than careful testing.
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Underground
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Teyla introduces the rest of the team to the Genii, whom she believes to be a peaceful, friendly folk. But the Genii have been hiding their true selves -- and their military organization -- the whole time the Athosians have known them. An attempt at an alliance goes wrong thanks to distrust on both sides, and by the end, the Genii and Atlantians have managed to make enemies of each other.
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Home
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The team discovers a world covered in mist that appears to be generating free-form energy -- enough to power the local stargate for an inter-galactic trip. When Weir and the team return to do just that, so they can at least send a message, the local energy beings -- the mist -- intervene to save their own lives, millions of which would be lost to power such a wormhole. The false realities they create are flawed, though, and eventually the team figures out that something here isn't right.
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The Storm
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When a megastorm is spotted headed for Atlantis, McKay and Zelenka search for a way to save the city, Ford and Sheppard negotiate a temporary refuge with the Manarians, and everyone else, including the Athosians, starts evacuating. But the Manarians trade the information about Atlantis's vulnerability to the Genii, who decide it's a perfect time to stage an attack.
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The Eye
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The Genii, led by Commander Kolya, have taken the city and are holding Weir and McKay hostage, leaving Sheppard alone to try to stop them. He engages in a running battle with Genii soldiers as McKay and Weir do their best to bluff and stall Kolya to buy him time. Meanwhile, the storm is getting ever closer.
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The Defiant One
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On a mission to explore a satellite that Dr. Gall discovered in the Atlantica solar system -- which turns out to be an Ancient weapons platform -- Sheppard, McKay, Gall, and Abrams find a 10,000-year-old downed Wraith supply ship. Unfortunately, one of the Wraith is still alive, and he attacks Abrams and Gall, then gets control of the jumper, although he can't leave in it. Despite his best efforts, Sheppard can't kill him, and it takes an attack from space from a rescue jumper to save the day.
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Hot Zone
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A team of scientists has been exploring the city and outlying areas for structural damage after a storm, when two of them begin suffering severe hallucinations and die of brain aneurysms. Suspecting a viral agent, the expedition goes into voluntary quarantine while a medical team tries to figure out what the agent is, exactly. Eventually they realize it's a nanovirus, and the only way to stop it is to explode a naquadah generator in the atmosphere to generate a massive EM pulse that will kill all the nanites.
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Sanctuary
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Sheppard's team discovers a world with a powerful weapon against the Wraith and go to meet the locals, hoping to gain either a ZPM or a promise of refuge for people fleeing the cullings. The local high priestess denies them aid and refuge, but agrees to go back to Atlantis for more information. While there, she and Sheppard get involved, and McKay gets suspicious, eventually figuring out that she's an ascended Ancient. She leaves to protect the world she's been exiled to.
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Before I Sleep
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An elderly Elizabeth Weir is found in a stasis chamber and revived, and tells the story of the original expedition -- which died when Atlantis's shields failed on the ocean floor, flooding the city. Only Weir, Zelenka, and Sheppard escaped, in a time machine that brought them 10,000 years into the past, and only Weir survived that trip. She met the Ancients and helped one, Janus, with a plan to eke out more power from the city's systems, then went into stasis to help carry the plan out.
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The Brotherhood
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Working closely with the Daganians, McKay and the rest of the team are close to finding a ZPM left behind by the Ancients. The Genii have been spying on them, though, and Kolya shows up just as they make a key discovery, capturing them and hoping to gain the ZPM for himself. In the end, though, it's the Daganians who win the day and the ZPM, leaving the Atlantians to go home empty-handed. Meanwhile, a Wraith dart appears above Atlantis, taking out one puddlejumper and two people, then scanning the city and sending the information back toward some hive ships before self-destructing.
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Letters from Pegasus
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With the Wraith just a couple short weeks away from Atlantis, McKay figures out how to send a high-compression databurst back to Earth, and everyone starts recording personal messages to be sent as well. Meanwhile, Sheppard and Teyla have gone offworld to try to track the Wraiths's progress, and get involved with old friends of Teyla's on a planet that is being culled.
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The Gift
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Teyla begins having terrible nightmares about the Wraith, and seeks help to find out what's causing them. Eventually the search leads her and the team to an abandoned Wraith lab, where evidence comes to light that some humans in the Pegasus galaxy -- including Teyla -- have some Wraith DNA thanks to human experimentation. Along with the DNA comes the ability to hear Wraith thoughts, and Teyla agrees to try to gain information about the fleet headed toward Atlantis. But while she's connected to the Wraith, the Wraith are also connected to her.
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The Siege, part 1
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With the Wraith just days away, the expedition searches for a safe alpha site, while a small team heads for the LaGrangian Point satellite hoping to repower the weapon to take out the approaching hive ships, and two teams head into the city to capture a Wraith that's been hiding out. The satellite takes out one hive ship, but is destroyed with Peter Grodin still aboard. With no other options, Weir orders the evacuation of the city to a newly discovered alpha site.
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The Siege, part 2
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The expedition begins evacuating the city, but before the last few leave, Colonel Dillon Everett arrives through the stargate from SGC, with personnel and weapons to aid in Atlantis's defeat, and the news that the Daedalus is just four days away. The Wraith attack begins in earnest, steadily cutting down Atlantis's defenses, both external and in terms of personnel, as Wraith have invaded the city proper by beaming in from darts. In the end, the city is left depending on Genii nuclear weapons in cloaked puddlejumpers as their final hope of holding out against the armada. But when the jury-rigged remote control system fails, Sheppard has to take one of the jumpers up himself in a suicide mission.
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