As Lt. Aiden Ford recovers from his near-fatal encounter with a Wraith, the team races against time to save the city from an impending Wraith assault.

A mysterious intruder has infected the Dadealus' computers with a virus that may allow them to take control of the ship.

Ronon Dex, a fierce survivor of a Wraith attack, may be the teama 's only hope in combating the now dangerous, Wraith-infected Ford.

A technical glitch during their rescue from a Wraith ship forces McKay and Lt. Cadman to coexist inside McKay's body.

While investigating a new planet, the team is ambushed by villagers. However, a strange craft appears, and rescues them. They learn the planet has a thriving and advanced society, despite the Wraith threat. The SGA team learns that they had been attacked by the worst prisoners on the planet. The prison they arrived on is also the location of the planeta 's Stargate The team finds this strange, but when they find out the truth of this conundrum they are conflicted. Things then go horribly wrong as they attempt to return through the prison islanda 's gate to consult with Dr. Weir.

McKay may have found a new and potent source of energy for Atlantis based on unperfected Ancient technology.

Team finds a planet that has had almost no Wraith culling in the last ten years, or since the time a Wraith ship crash there. However, they are told that one or two survivors must still be alive, as occasionally a villager dies in a culling way. Sheppard offers his teams help to kill the last of the Wraith for them, only to discover when they it, it is a young Wraith female, and she is with the villager who has been protecting her, and acting as her father. The team becomes intrigued by this pair when the father says the deaths could not have been from his daughter, as he has invented a drug that blocks a Wraitha 's need to cull on humans.

The team races to find a cure for the retrovirus that is mutating Sheppard into a Wraith.

The Atlantis team discovers a derelict Ancient spacecraft where the crew is in stasis. They attempt to awaken the crew, but find the Wraith have something to say about this. The question is whether the team can extricate themselves from this revival processes, and remove the Wraith from the equation.

Ford, who has survived being beamed aboard a Wraith ship, captures Col. Sheppard and his team. Ford has a daring plan to attack and destroy a Wraith Hive ship, and needs Col. Sheppard and McKaya 's knowledge and expertise to pull off the plan. Ford now has a following of converts who are also taking the Wraith enzymes, making them super soldiers too. What the Atlantis team doesna 't realize is, Ford has a plan that will require them to help him, or one of them will die. Things then go horribly wrong, leaving the team in a certain death situation. One must wait for part two to see if and how the team can survive Ford and his team and the Wraith!

After being captured during a failed attempt to destroy a Wraith hive ship, Ford, Sheppard, Teyla, Ronin, and some of Forda 's team try to figure a way out of their mess. McKay, who was left behind by Ford as insurance, tries to help the situation by taking a large dose the Wraith enzyme. This leads to a miss direction by the Wraith to Sheppard, and a battle between the Daedalus and two, not one, Wraith hive ship. Sheppard has a plan, but will it work before the Wraith destroy him, his team, or the Daedalus?

The team discovers a portal on a distant planet that pulls Sheppard to another world, where he encounters a dangerous creature. Back on the other side, McKay learns troubling news about the portal.

Atlantis is threatened by a bomb planted by the Goa'uld. Meanwhile, two Wraith cruisers are on course for the ancient city and a saboteur is unmasked.

McKay finds himself trapped in a Puddle Jumper which has crashed into the ocean and is sinking to the bottom. Col. Sheppard must not only locate McKay and the sinking missing Jumper before ita 's too late, but also must figure out a rescue strategy to reach the Jumper at the depths to which it is sinking.

Maj. Shepparda 's team travels to another planet in hope of finding an advanced technologic society to fight the Wraith, only to find another agrarian society. However, they do find the planet holds the one thing (well, several things) that they really need for Atlantis! However, the Lord Chamberlain of the ruler of the planet machinations put Maj. Sheppard and his team in jeopardy. Only McKay can prevent their demise. But his work endangers him, one of the town folk, the team, and the Tower! Will they survive?

Two pods are discovered that contain the minds of alien beings, who take control of Weir and Sheppard's bodies to continue their personal war.

Ladon, a Genii scientist who was involved with the Geniia 's attempt to capture Atlantis (S1E11: The Eye), contacts the SGA team to coerce them into helping him overthrow the Genii government he had been serving. His enticement is a zero point module that he has in his possession. The team decides it is worth risking the uneasy truce between the SGA and the Genii to acquire the ZPM. But, can they trust Ladon to keep his promise? Strangely, the SGA team finds they have their own ace card to play, when things start to go horribly wrong. To make matters worse, Maj. Lorne has gone missing while on an away mission. Telya and Ronon are sent to try and find out what happened to him.

A man is being treated by Dr. Beckett who apparently has amnesia. As he slowly recovers his memory, a major secret is revealed. Also, the secret that Atlantis was not destroyed and Teylaa 's life both become imperilled.

With no way out and trapped on a planet with a volcano, it is up to Dr. McKay to find a way to get the team out of there.

The Wraith, or at least one Hive ship, knows of Atlantisa ' survival. They learn Michael is on the ship, and finally communicate with him. He tells them that too many Wraith awoke to too few humans, and a civil war then broke out amongst the Wraith. Michaela 's faction wants to get a hold of Dr. Becketta 's retro virus in order to fight the other Wraith factions. They say they can survive by feeding on Wraith who have been converted to humans. Although the Atlantis team is reluctant to believe the Wraitha 's motives, they must take the risk to help Wraith in killing other Wraith. Things go horribly wrong, as the SGA finds the Wraith ship has a totally different agenda. Can Atlantis survive this betrayal? Things look dire for Atlantis! After all, they have given away their Wraith killing information, as well as the fact the Wraith know that Atlantis still exists.