The Atlantis expedition team, led by Dr. Elizabeth Weir, arrives in the Pegasus Galaxy and discovers the lost city of Atlantis. They encounter a powerful new enemy, the Wraith, and face various challenges to protect their new home while exploring the galaxy and seeking new allies.

As the Wraith threat intensifies, the team strives to find ways to defend Atlantis and the Pegasus Galaxy from impending invasion. Key episodes focus on breakthroughs in ancient technology, dangerous alliances, and a desperate search for a means to stop their enemies once and for all.

The team faces escalating conflicts with both old and new adversaries, including the Wraith and a deadly new faction. The discovery of a potential game-changing technology introduces new ethical dilemmas, while relationships within the team are tested under growing pressures.

With changes in leadership and new allies, the team continues to battle the Wraith and confront new existential threats. Personal dynamics shift as members struggle with loss and make significant choices that shape the fate of Atlantis and its mission in the Pegasus Galaxy.

As Atlantis faces its greatest threats yet, the team must rely on unexpected alliances and new technologies to safeguard their city and the galaxy. The season builds toward a climactic confrontation that tests the strength, ingenuity, and resolve of the entire expedition.