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Season Three
| No Mans Land - Episode 301 |
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The team desperately fight to try and stop two hives ships from reaching Earth. |
| Misbegotten - Episode 302 |
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The team must decide the fate of a colony of Wraith that have been turned back into human form as the result of Beckett's retrovirus. Meanwhile, Dr Weir is evaluted by the I.O.A regarding her leadership skills. |
| Irresistible - Episode 303 |
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Sheppard and his team discover a planet where a man called Lucius is worshipped by everyone. Its not long before members of the team seem to become in awe of him too. |
| Sateda - Episode 304 |
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Ronan is captured by the Wraith and once again, implanted with a homing device. He is released onto his home world so that the Wraith, can once more hunt him down and kill him. |
| Progeny - Episode 305 |
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Weir and the team travel to a planet that they believe are the home of the decendants, of the Atlantean people. However, once there, they discover that may not have left Atlantis in peace. |
| The Real World - Episode 306 |
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Weir wakes up in a mental institute and is told that the Atlantis expedition is merely a figment of her imagination. |
| Common Ground - Episode 307 |
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Sheppard finds himself a prisoner of Commander Kolya of the Genii. |
| McKay And Mrs Miller - Episode 308 |
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McKay is reunited with his estranged sister so that they can work together on a problem to harness power, using the math calculations his sister wrote. |
| Phantoms - Episode 309 |
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Sheppard and Ronan's minds are influenced by Wraith technology when a rescue mission for a lost team goes awry. |
| The Return (Part 1) - Episode 310 |
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The Atlantis expedition discover that a ship full of Ancients are returning to re-claim the City. |
| The Return (Part 2) - Episode 311 |
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Weir and her team defy orders and head back to Atlantis to save, the city, General O'Neill, and Richard Woolsey from the replicators. |
| Echoes - Episode 312 |
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Beckett witnesses a medical crew operating on a badly injured man, suddenly they disappear. Meanwhile, McKay experiments with a filter to understand what whales are saying, it turns out to be something familiar. |
| Irresponsible - Episode 313 |
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The team once again meet Lucius Lavin (last seen in Irresistible) on another planet, where he's posing as a super-hero. |
| Sunday - Episode 314 |
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A normal Sunday turns into something else after a bomb explodes on Atlantis. |
| TAO Of Rodney - Episode 315 |
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McKay gains some mental abilities that the others aren't able to grap, but in his eagerness to improve things, Zelenka gets hurt by a power surge. |
| The Game - Episode 316 |
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Sheppard and McKay's competitiveness in what they think is a game turns deadly when they discover that the game is infact real, and the civilizations they've been piting against each other are now on the brink of war. |
| The Ark - Episode 317 |
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The team discover a civilization in suspended animation. As some of them awaken we learn that they each have very different expectations of what's to come. |
| Submersion - Episode 318 |
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The team search deep under water for an alternative power source to the ZPM. |
| Vengeance - Episode 319 |
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The team go in search of some missing allies, but instead find an old foe creating a race of powerful monsters. |
| First Strike - Episode 320 |
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Earth launches an attack on the replicators home world Asuran, but in doing so, put Atlantis at risk. |