Atlantis is saved in the nick of time by the Daedalus, who manages to destroy the other two Hive Ships. However, 12 more are on their way, and they quickly adapt to the Tau'ri's measures. Meanwhile, the team find Lt.Aiden Ford, who has an overdose of the Wraith enzyme.
After a return journey from Earth back to Lantea, an unexplained death happens on board the Daedalus. He was killed when he figured out that a Wraith computer virus has uploaded itself into the Daedalus' computers, and is taking over the ship.
After finding a dead Wraith on P3M-736, the Atlantis expedition find evidence that a missing Aiden Ford is responsible. When searching for him, it is not only Ford they find.
After being scooped up by a Wraith Dart, Dr.Rodney McKay is rescued, but there isn't enough power to recover Lt.Laura Cadman. Soon, McKay realizes that Cadman's consciousness is inside of him, and the two have a hard time in co-existing. Ronon Dex makes himself at home in Atlantis.
Lt. ColonelJohn Sheppard's team is ambushed by unfriendlies when they are rescued by a technologically advanced civilization. They learn that the people on "the Island" are convicts, so the Wraith cannot feed on the innocent.
The team find an outpost on an uninhabited planet, and find that the Ancients were researching a power source which would render Zero Point Modules obsolete. Meanwhile, Ronon Dex learns that not all Satedans were killed during the Wraith attack.
Lt. ColonelJohn Sheppard's team find a civilization haunted by a string of mysterious periodical killings, by the "Daimos", a Wraith. While hunting it down, they find a young female Wraith named Ellia, who's "father" Zaddik apparently found a serum to stop her need to feed.
The team are captured by Wraith, and notice that a second Hive Ship is joining them. Meanwhile, Dr.Rodney McKay manages to escape his captors and returns to Atlantis, where they resume the search for the rest of the team.
Lt. ColonelJohn Sheppard's is sucked through the event horizon of an entrance to a cave, and cannot get out the same way. Worse, there is a Time dilation field, meaning that minutes in relative conditions could mean hours for Sheppard. If they don't find a way to save him soon, he is going to die of old age.
The NID pick up intelligence that The Trust has not only heard of Atlantis, but has been there, and the Goa'uld has planted a bomb in the city that is sent to go off the next time the expedition dials Earth.
Lt. ColonelJohn Sheppard's team visits a planet where they encounter a City-ship buried under foliage, and the central tower is used by the royalty of the planet. The Lord Protector is using an AncientControl chair to rule over peasants near to the planet. He is dying and his children now compete for the throne.
Lt. ColonelJohn Sheppard's team finds two pods adrift in space. When they recover them, they find an aged person in each one. The two consciousnesses make it into Sheppard and Dr.Elizabeth Weir, and convince the team that they are old lovers. However, the two are actually enemies trying to kill each other over a war that ended a long time ago.
Ladon Radim of the Genii contacts Atlantis and wants their help in staging a coup against Cowen, in exchange for a Zero Point Module. However, not all has changed since the expedition's last encounter from the Genii.
Lt.Michael Kenmore wakes up with no memories about who he is, after he was supposedly captured by the Wraith. While trying to remember his past life, he notices that everyone is looking at him strangely. Soon, he discovers the hard way that he wasn't captured by the Wraith, but was one himself.
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