: After the failed retrovirus experiment in Season 2, Michael becomes a rogue agent. He begins experimenting with Iratus bugs to create his own army, positioning himself as a common enemy to both humans and Wraith.
Season 3 of Stargate Atlantis (2006–2007) is widely considered a turning point for the series, shifting from episodic exploration toward complex, multi-factional warfare and deeper character-driven drama. The season introduces the (human-form Replicators) and deepens the threat of the Wraith-human hybrid, Michael . Major Story Arcs
: Initially mistaken for surviving Ancients, the Asurans are revealed as Replicators created by the Ancients to fight the Wraith. This arc culminates in the two-part episode "The Return," where the Ancients briefly reclaim Atlantis before being massacred by the Asurans , forcing the Earth expedition to retake the city.
: The season explores the moral complexities of Earth’s involvement in the Pegasus Galaxy. This includes the implementation of the McKay-Carter Intergalactic Gate Bridge and the introduction of the battle-cruiser Apollo , which carries out a controversial preemptive strike against the Asuran homeworld. Key Characters & Milestones Atlantis Season 3 | SGCommand | Fandom