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.
Detective John Sheppard investigates a series of unusual murders in Las Vegas.
Dr. Keller suffers the ultimate form of identity theft when her strange behavior leads the team to discover that her consciousness has been switched with that of a criminal who is facing capital punishment.
McKay returns to Earth to witness the unveiling of his rival's latest breakthrough.
While exploring the mainland of Atlantis' planet, Sheppard is captured by a foe believed to be long dead.
Michael besieges Atlantis in an attempt to kidnap Teyla's infant child.
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.
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.
Sheppard must rescue McKay and Daniel Jackson from an Ancient laboratory that belonged to Janus before Todd, who has hijacked the Daedalus, gets there first.
Daniel Jackson visits Atlantis to do some research on the Ancient scientist Janus.