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 the 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 Advisor's. 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. Written by Mark Ernst

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 after they've deployed the Retrovirus and all the Wraith has been converted into Humanoids again. Tayla contacts Cayenne through the gate and briefs Weir of their current status. It appears that a Hive is approaching, which later on appears that it's controlled by Sheppard and Michael. While Weir struggles with the IOA, Richard Woolsey, they've re-deployed the retrovirus on Michael and once again, put the earlier converted Wraith on a planet and monitor their status. Suddenly, a former Wraith gets murdered and the situation escalates further from there on out. Written by Mark Ernst

The new plan of the McKay-Carter Subway 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. Written by Mark Ernst

Sheppard and his team visit a planet but Ronon feels that he's been there before. In his days as a runner, the Wraith had hunted him there, causing much destruction and resulting in the death of the local leader's daughter. They haven't forgotten and soon have the entire team in captivity. Turned over to the Wraith, Ronon is once again forced into being a runner and they return him to his home planet of Sateda. In flashbacks, key events in Ronon's previous life are revealed. Needless, his friends don't just sit by idly but head to Sateda to help him. Written by garykmcd

The Atlantis team receive a response to one of their probes from a society that seems to be the Ancients. Elizabeth Weir joins Sheppard, McKay and the rest of the team to meet them. To their amazement, they find another city very much like Atlantis only larger and more elaborate with millions of residents. The group's leader, Oberoth, says they left Atlantis many years before after a dispute and created a new life for themselves. McKay is amazed to learn that they have a virtually unlimited number of ZPMs to power the city. Elizabeth wants to discuss trade and the establishment of diplomatic relations but Oberoth seems uninterested. The Atlantis team soon discovers that all is not as it seems. Written by garykmcd

Dr. Elizabeth Weir wakes up in a locked hospital room only to be told that she is in a psychiatric institute on Earth. She's also told that her entire experience on Atlantis was a dream. Even Jack O'Neil professes to have no knowledge of Atlantis or of any such thing as the Stargate program. It all seems to be very real to her. Her mother visits and she even sees her pet dog. She also sees shadows at night that are quite frightening but seem to be trying to communicate with her. She is convinced that her time on Atlantis was real and that it is her current reality that is false. Written by garykmcd

Sheppard is taken prisoner by his old nemesis, Commander Kolya of the Genii. He finds himself in a dungeon occupying a cell next to a Wraith who says he has been there a very long time. Kolya had expected to become the leader of the Genii but was ousted by Ladon Radim and is now a renegade. He contacts Atlantis and has a simple proposition for Dr. Weir: hand over Ladon Radim, with whom Weir has entered into a truce, and Sheppard will be freed. Weir flatly refuses so Kolya allows the Wraith to feed off Sheppard for a few seconds at a time, and he begins to age dramatically as a result. He broadcasts Sheppard's torture sessions to Atlantis so they can see the result of Weir's decision. While Weir and the others on Atlantis try desperately to find the planet where Kolya is keeping Sheppard prisoner, the Colonel forms a strange bond with the Wraith who work together to escape. The Wraith also shows him a power that no one from Atlantis knew they had. Written by garykmcd

Rodney McKay returns to Earth to visit his sister, Jeannie Milller, after she solves a mathematical proof that may provide for a means for transferring particles to a parallel universe. They need her help to further determine the practical aspects of her theory but she refuses to sign a non-disclosure agreement. She quite surprised to see Rodney on her doorstep given that he has not been in touch with her for four years. He manages to convince Jeannie to cooperate by transporting her to the Daedalus and soon they are in Atlantis working on the problem. There is more than just a little sibling rivalry between the two and she regales everyone with tales from Rodney's youth, not the least of which is that Rodney is his middle, not his first, name. Their attempt at transporting particles to a parallel universe goes somewhat awry when Rodney's doppleganger suddenly appears. The alternate Rodney has a somewhat different personality from the Rodney everyone knows - funny and self-effacing ... Written by garykmcd

When a team led by Major Leonard is late in returning, Sheppard leads a mission to find what may have happened to them. They find three of the team dead as well as evidence that Major Leonard was responsible for killing his own men. Finding themselves under attack by the errant Major and with several Marines wounded, Sheppard, Teyla, Ronan, McKay and the others begin to hallucinate. The source of the problem is an experimental Wraith pulse generator but McKay is having trouble turning it off. With Sheppard fighting an imaginary battle in Afghanistan and Ronan an imaginary Wraith - they're actually shooting at each other - it's left to Teyla to sort it out. Written by garykmcd

The day Rodney McKay has long been waiting for finally arrives: the inaugural test of the interstellar subway that will link the Pegasus and Milky Way galaxies. Arranged as a series of interconnected gates, the traveler only stops at a mid-way transfer station. With Sheppard at the controls of a puddle jumper, the test is uneventful and works quite well. McKay does catch one anomaly however - a passing ship traveling just below the speed of light, apparently belonging to the Ancients. When they make contact, they learn that the Ancients' ship had lost its hyper-drive and the Daedalus offers assistance. Once back on Atlantis, the Ancients have only one request - that the Earthlings leave Atlantis immediately. The Replicators however also have their eye on the city Written by garykmcd

Apparently able to reprogram their base code, the Replicators have attacked and defeated the Ancients who had only recently taken over control of the city. General O'Neil and Richard Woolsey had stayed behind to negotiate with the Ancients and are hiding out in a remote part of the city. It doesn't really matter however since O'Neil's standing orders are that Atlantis is to be destroyed with a nuclear device should it ever be taken over by hostile forces. Sheppard, Weir, McKay and Beckett collect Teyla and Ronon Dex en route and devise a plan to surreptitiously enter the city and rescue their colleagues. If they are to be successful McKay will also have to find a way to destroy the Replicators before they reprogram themselves and make their weapons useless. Written by garykmcd

Teyla is shocked when she sees the ghostly image of a woman in the corridors of Atlantis. The woman is an Ancient in appearance but, initially at least, no one else can see her. Others begin to have their own visions however. Dr. McKay is enjoying himself watching a whale-like creature that is swimming just off the city. He's certain that it's the same creature who guided Sheppard to save him when he was trapped on the ocean floor. He nicknames the creature Sam, after his good friend Samantha Carter. When hundreds of the sea creatures are found to be heading for Atlantis, clearly something is wrong. McKay's search of the alien database reveals that Atlantis is under threat of destruction. Written by garykmcd

Sheppard and his team visit a planet where there supposedly lives a great hero, someone who has great powers. They arrive to find that the great hero is none other than their old friend, Lucius Lavin. they immediately suspect that he's seduced the locals by using his drug but that proves not to be the case. He does have a body shield however that seems to make him impenetrable. As his popularity begins to wane, a group of bandits attacks the village. He repels them and is once again the hero. The bandits turn out to be outcast Genii warriors, part of the late Cowan's personal bodyguards who were actually being paid by Lucius to stage a phony attack. When Lucius stiffs them on the agreed payment, they return for real this time with commander Kolya in charge....and he would like nothing better to get his revenge on Sheppard. Written by garykmcd

After a time when the Ancients have been shortly living in Atlantis, they have activated a whole bunch of equipment and devices. The Atlantis researchers team is walking around the city to shut it all down again. Suddenly they discover an old research terminal and McKay is going to try to shut it down. Although that does not quite happen like it should. Written by Mark Ernst

Since soon after their arrival in Atlantis some 2 years ago, McKay and Sheppard have been playing a computer game. The game has two civilizations, separated by a river, with McKay and Sheppard tasked to see who can build the better society. McKay's approach is give his society more and better technology while Sheppard's solution is to increase the size of his society's army. They soon learn however that what they have been playing is not a game, but real societies who, until their intervention, lived in a state of peaceful co-existence. After nearly two years of meddling however, they are now on the verge of war. Written by garykmcd

On a distant moon, Sheppard, McKay, Ronon Dex and Teyla find an elaborate subterranean base. The technology is anything but up to date and the base seems to be abandoned, until McKay decides to restore power. When he does so, a scientist materializes and it would seem that he had developed a means of using transporter technology to store a person's essence. The technology was developed to save as many of their people as possible from the Wraith culling and there are several thousand of them in stasis. As the decrepit station begins to fail, Teyla is pulled into stasis by one of the surviving scientists forcing Sheppard to risk his own life to save all of them. Written by garykmcd

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. The Sunday, a day like no other, suddenly turns bad and it appears that a lot of people are in danger. Written by Mark Ernst

The team locates a mobile geothermal drilling platform that may have the potential of providing them an unlimited power supply. Before going too far ahead, Dr. Weir wants to learn why the Ancients abandoned the project. On arrival, Teyla immediately begins to sense a Wraith presence on the platform. Her attempt to contact the Wraith doesn't quite go as planned however, and she is soon under a Wraith Queen's control. Weir and the team soon learn that the Wraith Queen has been waiting for millenia for a means to escape the ocean's depths and return to her people....and will stop at nothing to accomplish that. Written by garykmcd

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. Written by Jono Hayward

Col. Abe Ellis arrives at Atlantis with a new ship, the Apollo, and important news: a new Replicator base has been detected and it appears they have been building a new fleet of ships. He is under orders to destroy the Replicator base and while Dr. Weir doesn't agree with the plan and would prefer to negotiate with them, it's clear that the decision has already been made. The mission seems to go off without a hitch but when a gate appears above Atlantis, the city finds itself bombarded with deadly ray. Their first attempt at saving the city proves to be temporary at best and they are left with only one choice: activate the city's hyper-drive and leave the planet. Meanwhile, having been bypassed in the decision to attack the Replicators in the first place, Dr. Weir questions whether she can continue as head of mission but fate intervenes. Written by garykmcd