UNDERGROUND

Teyla introduces the Atlantis team to the Genii, though she doesn’t know who the Athosians’ long-time ally really is. After McKay and Sheppard discover the Genii’s underground city, they confront their leader Cowen with the critical question: Are we going to be allies, or enemies?

The team join the Genii on a dangerous mission inside a Wraith hive, and the results will more or less seal the future of the alliance … for good or for ill.

THE STORM

Cowen’s mind is set against Atlantis, and intel from one of the Genii’s many spies provides a unique opportunity. The Atlantians are temporarily evacuating the city of the Ancestors due to an imminent storm. He orders his top General, Acastus Kolya, to lead a strike team to penetrate the city’s defenses and steal its valuable technology and munitions before the storm hits.

THE EYE

Commander Kolya’s mission to steal from Atlantis — and even take control of the city itself — does not go according to plan when John Sheppard kills most of his strike force. With Weir and McKay held at gunpoint, Kolya tries to force Sheppard to give him what he wants.

Their final confrontation is sure to end with more bloodshed, and cement a bitter rivalry between the two men.

THE BROTHERHOOD

When Sheppard’s team goes in search of a lost Zero Point Module on the planet Dagan, Kolya and his spies aren’t far behind. As Rodney works alongside the beautiful Allina to solve the ancient mystery of the Quindosim, the Genii plot to steal the Z.P.M. for themselves.

THE SIEGE, PART 2

Despite the fact that the Genii can never be trusted, and despite the recent hostilities, there is still one thing that Atlantis and the Genii have in common: their shared enemy. The Wraith finally come to Atlantis in the season finale, and a rapidly draining shield is the only thing standing between our heroes and total annihilation.

After backup arrives from Earth, Weir is pressed to the only course of action left to her: she visits the Genii to try and secure nuclear weapons. There she faces interrogation by Prenum, a Genii officer who isn’t about to give up something so valuable.

COUP D’ETAT

It’s a turning point for the Genii as a people, as an ambitious young officer named Ladom Radim — who was part of Kolya’s team during the assault on Atlantis — hatches his own scheme. Ladon tells Atlantis that he has defected from the Genii, offering them a Z.P.M. if they will arm his efforts to overthrow Cowen. But is Ladon working with Atlantis against Cowen, or working for Cowen to betray Atlantis?

COMMON GROUND

Kolya and his closest loyalists capture John Sheppard during an off-world mission, and radio Atlantis with their demands: hand over Ladon Radim. Kolya reveals that Ladon’s coup disrupted his own plans to take control of the Genii, and now he wants revenge.

Using a captured Wraith, Kolya subjects Sheppard to brutal torture — having the life drained out of him. As John loses years and then decades off his life, his feud with Kolya grows more bitter and more deeply personal than ever before.

IRRESPONSIBLE

Sheppard’s team finds an unexpected face inside a village that is being terrorized by mercenaries: their old friend Lucius Lavin, a con man and coward who has found himself an Ancient personal shield emitter. He’s using it to put on a good show with the hooligans he has hired — but these men are actually proud Genii, former members of Cowen’s personal guard.

Eventually the Genii call upon an ally to deal with Lucius: none other than Commander Kolya himself. And when he finds Sheppard’s team, all bets are off.

HARMONY

Colonel Sheppard and Dr. McKay enjoy a pleasant visit with one of Atlantis’ favorite trading partners, and agree to play chaperones when they learn that the local princess — young Harmony — must journey through the forest to the Temple of Laros before she may be crowned the new queen.

Their excursion proves to be not so simple when they find that the biggest threat to Harmony isn’t the local animal life in the forest, but a contingent of Genii soldiers who are trying to stop her from ascending to the throne.

INQUISITION

A new coalition of planets in the Pegasus Galaxy are ready to join together in common cause against the Wraith, and they invite Atlantis to send representatives. But when Sheppard and his team arrive they are taken into custody, and put on trial for their many “crimes” against the peoples of this galaxy (starting with being the ones who woke up the Wraith to begin with).

Eventually Richard Woolsey, Atlantis’ new expedition leader, uses his legal skills to come to the team’s defense … and he learns that the Genii are really the ones behind the trial.

REMNANTS

The worst kind of enemy is the one who doesn’t stay buried. Years after he thought he had dealt with Acastus Kolya once and for all, John Sheppard is shocked to come face-to-face with his nemesis while on an ordinary survey mission on the mainland. John is beaten mercilessly, but refuses to give his iris code to the enemy.

How can Kolya not only be alive, but running around Atlantis’ new home planet with a squad of Genii? Sheppard will eventually learn that there is something going on here far beyond his control, with connections to an ancient alien race seeking to be reborn.