Because McKay is helping the Wraith Hive with the implementation of the retrovirus, Ronan also stays on board. Appearing later on, the Hive betrays the Atlantis Team and the as they try to take out the Daedalus, they both deploy their fighters. Sheppard takes an X302 and hooks onto the hull of the Hive. Weir orders the Daedalus and the Orion to engage the Hive fleet and is being recalled to Cheyenne Mountain to brief the Internal Oversight Advisor's. Back in Pegasus, Sheppard tries to contact McKay and Ronan over the COM but Michael picks up and elaborates on his ...

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Because of the earlier battle, Daedalus has been severely damaged and life-support is minimal at best, they decide to transport everyone onto the Wraith Hive after they've deployed the Retrovirus and all the Wraith has been converted into Humanoids again. Tayla contacts Cayenne through the gate and briefs Weir of their current status. It appears that a Hive is approaching, which later on appears that it's controlled by Sheppard and Michael. While Weir struggles with the IOA, Richard Woolsey, they've re-deployed the retrovirus on Michael and once again, put the earlier...

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The new plan of the McKay-Carter Midway Station is under way. The Atlantis Team needs to harvest space gates in order to form the Galactic Bridge. Sheppard disagrees with McKay's plan to steal the gates and they go in for first contact with the "back water hamlets" as McKay calls it. As they walk into the city, they are greeted by a man called Lucius, who has the locals eating out of his hand. Everyone is hanging on this man's every word and so is Carson. He's completely smitten with him and Lucius now knows the location and the thriving existence of Atlantis. It ...

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After a group of people capture and give Ronon to the Wraith, he becomes a runner again, but this time he's left in his home planet, Sateda, where the Stargate has been disabled.

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The Atlantis expedition encounters a highly advanced race, the Asurans. They initially believe them to be the Ancients. However, this new race is just a new face of an old nemesis.

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Dr Weir finds herself on Earth where, to everyone else, the Atlantis Expedition was just her delusion.

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John Sheppard is kidnapped by the Genii and is in the company of a Wraith.

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Rodney's sister is brought to Atlantis to make use of one of her theories.

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A device that creates hallucinations affects the team off-world.

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The Atlantis expedition must turn to an old friend for help as the Asurans prepare to invade the city.

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The team returns to Atlantis in an attempt to regain control of the city.

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Teyla witnesses what appear to be an Ancient apparitions, which soon other people start to see.

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The team investigate rumours of an invincible hero off-world, only to find Lucius Lavin again manipulating a hapless village.

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When Rodney uses an Ancient device, he gets special powers, but soon Dr Weir discovers it's a double-handled gift: if he doesn't ascend, he'll die.

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The Atlantis team finds a program in the Atlantis database which throws Mckay and Sheppard into a Simsesque game that could destroy two civilizations in the Pegasus Galaxy.

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The team boards a crippled space station to discover people have been preserved there with the hope to outlive their enemy, the Wraith.

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Almost every member of the Atlantis expedition has a day off. Some of them are enjoying their free time or are catching up on some old work. The Sunday, a day like no other, suddenly turns bad and it appears that a lot of people are in danger.

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The Atlantis team finds an Ancient underwater research facility and puts a team together to check it out.

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After losing contact with the new Taranin (the people rescued by the Atlantis team when a super volcano threatened to destroy their planet) settlement, Sheppard's team leaves to investigate. Finding the town deserted, they move to investigate an extensive subterranean tunnel system. What they find there holds dark tidings for the entire Pegasus Galaxy.

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After learning the Asurians are building a fleet of ships, Earth sends its newest ship, the Apollo, under the command of Colonel Abe Ellis to initiate a preemptive first strike to stop them from attacking Atlantis or worse, Earth itself.

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