3.01 – No Man’s Land

(July 14, 2006) Directed by: Martin Wood

Because McKay is helping the Wraith Hive with the implementation of the retrovirus, Ronan also stays on board. Appearing later on, the Hive betrays the Atlantis Team and then as they try to take out the Daedalus, they both deploy their fighters. Sheppard takes an X302 and hooks onto the hull of the Hive. Weir orders the Daedalus and the Orion to engage the Hive fleet and is being recalled to Cheyenne Mountain to brief the Internal Oversight Advisors. Back in Pegasus, Sheppard tries to contact McKay and Ronan over the COM but Michael picks up and elaborates on his current status within the Hive and start working together to bring down the Wraith Hives.

3.02 – Misbegotten

(July 21, 2006) Directed by: Martin Wood

Because of the earlier battle, Daedalus has been severely damaged and life-support is minimal at best, they decide to transport everyone onto the Wraith Hive ship after they’ve deployed the Retrovirus and all the Wraith have been converted into Humanoids again. Teyla contacts Cheyenne through the gate and briefs Weir of their current status. It appears that a Hive ship is approaching, which turns out to be controlled by Sheppard and Michael. While Weir struggles with the IOA liaison Richard Woolsey, they’ve re-deployed the retrovirus on Michael and put him and the converted Wraith on a planet to monitor their status. Suddenly, a former Wraith gets murdered and the situation escalates.

3.03 – Irresistible

(July 28, 2006) Directed by: Martin Wood

The new plan of the McKay-Carter Midway Station is under way. The Atlantis Team needs to harvest space gates in order to form the Galactic Bridge. Sheppard disagrees with McKay’s plan to steal the gates and they go in for first contact with the “back water hamlets” as McKay calls it. As they walk into the city, they are greeted by a man called Lucius, who has the locals eating out of his hand. Everyone is hanging on this man’s every word and so is Carson. He’s completely smitten with him and Lucius now knows the location and the thriving existence of Atlantis. It appears, as Lucius explains, that he has an herb that makes him appealing to everyone. He later on exploits this until the locals experience withdrawal symptoms from the herb and they grow sick. Everyone in Atlantis is smitten and do what ever he wishes. Sheppard has totally had it and kidnaps Carson and forces him to make an antidote, while he is still in withdrawal.

3.04 – Sateda

(August 4, 2006) Directed by: Robert C. Cooper

After a group of people capture and give Ronon to the Wraith, he becomes a runner again, but this time he’s left in his home planet, Sateda, where the Stargate has been disabled.

3.05 – Progeny

(August 11, 2006) Directed by: Andy Mikita

The Atlantis expedition encounters a highly advanced race, the Asurans. They initially believe them to be the Ancients. However, this new race is just a new face of an old nemesis.

3.06 – The Real World

(August 18, 2006) Directed by: Paul Ziller

Dr Weir finds herself on Earth where, to everyone else, the Atlantis Expedition was just her delusion.

3.07 – Common Ground

(August 25, 2006) Directed by: William Waring

John Sheppard is kidnapped by the Genii and is in the company of a Wraith.

3.08 – McKay and Mrs. Miller

(September 8, 2006) Directed by: Martin Wood

Rodney’s sister is brought to Atlantis to make use of one of her theories.

3.09 – Phantoms

(September 15, 2006) Directed by: Martin Wood

A device that creates hallucinations affects the team off-world.

3.10 – The Return: Part 1

(September 22, 2006) Directed by: Brad Turner

The Atlantis expedition must turn to an old friend for help as the Asurans prepare to invade the city.

3.11 – The Return: Part 2

(April 13, 2007) Directed by: Brad Turner

The team returns to Atlantis in an attempt to regain control of the city.

3.12 – The Return: Part 2

(April 20, 2007) Directed by: William Waring

Teyla witnesses what appear to be an Ancient apparitions, which soon other people start to see.

3.13 – Irresponsible

(April 27, 2007) Directed by: Martin Wood

The team investigate rumours of an invincible hero off-world, only to find Lucius Lavin again manipulating a hapless village.

3.14 – Tao of Rodney

(May 4, 2007) Directed by: Martin Wood

When Rodney uses an Ancient device, he gets special powers, but soon Dr Weir discovers it’s a double-handled gift: if he doesn’t ascend, he’ll die.

3.15 – The Game

(May 11, 2007) Directed by: William Waring

The Atlantis team finds a program in the Atlantis database which throws Mckay and Sheppard into a Simsesque game that could destroy two civilizations in the Pegasus Galaxy.

3.16 – The Ark

(May 18, 2007) Directed by: William Waring

The team boards a crippled space station to discover people have been preserved there with the hope to outlive their enemy, the Wraith.

3.17 – Sunday

(June 1, 2007) Directed by: William Waring

Almost every member of the Atlantis expedition has a day off. Some of them are enjoying their free time or are catching up on some old work. Then Sunday, a day like no other, suddenly turns bad and it appears that a lot of people are in danger.

3.18 – Submersion

(June 8, 2007) Directed by: Brenton Spencer

The Atlantis team finds an Ancient underwater research facility and puts a team together to check it out.

3.19 – Vengeance

(June 15, 2007) Directed by: Andy Mikita

After losing contact with the new Taranin (the people rescued by the Atlantis team when a super volcano threatened to destroy their planet) settlement, Sheppard’s team leaves to investigate. Finding the town deserted, they move to investigate an extensive subterranean tunnel system. What they find there holds dark tidings for the entire Pegasus Galaxy.

3.20 – First Strike

(June 22, 2007) Directed by: Martin Wood

After learning the Asurians are building a fleet of ships, Earth sends its newest ship, the Apollo, under the command of Colonel Abe Ellis to initiate a preemptive first strike to stop them from attacking Atlantis or worse, Earth itself.