When Sheppard and his team are about to return from an off world mission with their Puddle Jumper, the systems of the Jumper go crazy. Barely able to return to Atlantis, the Jumper seems to infect the city's systems with what seems to be a computer virus.
When the Wraith discover that a small group of survivors of Michael's release of the modified Hoffan drug are hiding among the population of a village on another planet, Sheppard and his team must convince the entire village to evacuate before a Hive Ship arrives.
When Sheppard and his team are brought to trial by a Coalition of human worlds for what they claim are crimes against the people of the galaxy, it's up to Woolsey's legal expertise to clear their names.
While exploring the mainland of Atlantis' planet, Sheppard is captured by a foe believed to be long dead. Meanwhile, Woolsey's job is at risk and he has an important decision to make and McKay and Zelenka make an interesting undersea discovery.
A thief uses an Ancient transfer device to switch her consciousness with Dr. Keller. While she attempts to escape Atlantis, Dr. Keller must deal with the thief's accomplices and angry villagers on her trail.
Todd informs Atlantis that a rogue Wraith has acquired several Z.P.M.'s to power a formidable new Hive ship. When the Daedalus engages it in battle but is unable to defeat it, the team gets a message indicating it is headed to Earth.
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