After the explosion of Michael's medical compound, which caved in, trapping the Atlantis team and the marines, Colonel Samantha Carter sends a rescue party along with a medical team and the combat engineers, as well as a new addition to the Atlantis team, Captain Alicia Vega. As the rescue starts, it appears that the team has been split into the two surviving groups of Ronan and Lt. Colonel Sheppard, and McKay and Major Lorne. When McKay finds Michael's hard drive, it contains a lot of data about his operations. Suddenly, McKay realizes that, when the compound self destructed, it sent out a subspace message that alerted Michael of their presence. With the Daedalus now in orbit, Michael appears and they engage into combat. As the battle progresses, they realize that Teyla could be aboard and they decide to mount a rescue mission to retrieve her. When they're aboard, it appears that Teyla is nearing birth and they'll have no chance of retrieving her in time. Written by Mark Ernst

While working with the information retrieved from Michael's medical compound and trying to find a solution to the cellular degeneration of the cloned Dr. Beckett, Jennifer Keller becomes infected with a Wrath virus. Beckett is taken out of stasis and put in charge of finding a solution to the problem by Richard Woolsey who has, to everyone's surprise, replaced Samantha Carter as the base commander. As the virus host, Jennifer is the central being in a growing life form that is literally climbing the walls and spreading. Beckett thinks he has the cure the it will take someone to administer it, a life-threatening situation. Written by garykmcd

Ronon is kidnapped by a Wraith who has every intention of turning him into a warrior for the Wraith cause. He has had considerable success in using drugs and torture to brainwash others. One of them, Tyre, is discarded by the Wraith when they think he is no longer of use to them. Tyre is rescued and taken back to Atlantis for painful detoxification and he agrees to lead them back to rescue Ronan. Teyla meanwhile is struggling with her own competing loyalties as she must decide whether to remain a member of Sheppard's team or concentrate on being a mother to her newborn child. Written by garykmcd

Everyone on Atlantis is shocked when the Daedalus, which is supposed to be en route to Earth, suddenly appears in orbit above the city. Sheppard and his team go aboard and find their doubles, all dead. McKay concludes that the ship is from an alternate dimension and in the wink of an eye, they are transported to an alternate reality. The first jump has them trying to figure out where they are while McKay tries to determine why the ship is acting as it is. Their second jump sees them under attack from an unknown race and the third jump has them too close to sun and under risk of being burned up. McKay concludes that the only way they will ever again see their own Atlantis is to travel back through each of the jumps they have just made. Written by garykmcd

Returning from an off-world mission in a puddle jumper, Sheppard, Teyla, Ronan and McKay suddenly find themselves in a ship that swings wildly between complete power failure and power surges that are blowing out some of the ship's systems. When they manage to get back to Atlantis, a diagnostics check reveals no problem whatsoever with the jumper. Soon however, systems across the city are affected in the same way. McKay is having difficulty isolating the source but it finds him by shutting down all but his computer. When he finally manages to communicate with it, he and everyone else is in shock at who it claims to be. Written by garykmcd

While on an off-world mission, Rodney McKay acquires a parasitic organism and over a period of a few weeks, degenerates into a child-like reverie. His sister Jeannie travels to Atlantis to be with him in what everyone believes will be his final few days. Ronan however recalls a fable from his youth of a shrine where people reverting to their childhood much like McKay could go with their friends and family and become lucent for one last day. It works but McKay isn't too keen on it being his last day of life and Dr. Keller suggests thew only other option is for her to operate. Written by garykmcd

After an an off-world team led by Maj. Anne Teldy finds what appears to be one of Michael's abandoned laboratories, Sheppard and Dr. Beckett travel to the planet to see for themselves. It's not obvious why the lab has been abandoned since the information in the computer system seems to indicate that Michael's experiments had been successful. The village is empty and they have no idea what may have happened to the residents - until they find 12 empty pods and have to assume there are a dozen human-Wraith hybrids now roaming the area. Just as they think they've gained the upper hand however, they discover something in a hidden room. Written by garykmcd

Sheppard, McKay, Teyla, Ronan and Jennifer Keller travel to a rendezvous with Todd the Wraith. Keller believes she has found a vaccine of sorts to modify the Wraith at a genetic level that will render it unnecessary for them to feed on humans. She needs test subjects however and Todd agrees but indicates that they will have to seek the support of the Queen of an allied Wraith hive. Since his own Queen has been killed, it will be necessary for someone to impersonate her - and the only person able to get away with that would be Teyla. She agrees but once on board the allied ship, it's very clear that Todd hasn't been entirely forthcoming as to his exact plan. Written by garykmcd

Ronan and McKay accompany Jennifer Keller who is going off-world to provide needed medical services. McKay is hoping to have some time alone with her and is disappointed when he realizes that Ronan is coming along as well. Once there, Jennifer is kidnapped by a runner who wants her to give medical care to a very special patient. Ronan and McKay are soon tracking her however and having to fight the Wraith who are after the runner. Written by garykmcd

Dr. Daniel Jackson comes to Atlantis in search of a lost Atlantian room. The discovery reveals a new race. Daniel and McKay are kidnapped by the new race and are forced to finish a device which may kill the Wraith. Todd feels betrayed and takes the Daedalus. Written by Anonymous

The new race that stole the device, not to mention Rodney and Daniel, turns out to be an old one meaning very old and well known to the human race. With an ancient grudge to settle they force Rodney to activate the device against the Wraith with a side effect that could kill millions through out the galaxy. That make the Wraith mad so they abscond with the Daedalus to retaliate. Once again we lowly humans have to take control of a messy situation to keep the master races from wreaking havoc in the galaxy. Written by David Foss

Sheppard and his team pay a surprise visit to Dr. Carson Beckett who is providing medical services in a small village. There are many refugees there, fleeing Wraith culling and the Wraith themselves are there but not feeding on anyone. It seems the refugees are all infected with the Hoff virus and any attempt at feeding will kill them. The residents themselves are divided on the fate of the refugees with some wanting to offer them protection and another faction wanting to turn them over to the Wraith in return for being left alone. The team's attempt to take the refugees off planet and back to Atlantis inevitably leads to a conflict with the Wraith. Written by garykmcd

Sheppard and his team are lured to a planet and are soon put on trial for crimes against the people of the Pegasus galaxy. In flashbacks, the three judge tribunal recounts the indictment against them including the re-awakening of the Wraith and the various missions where at least a few, if not more, innocent bystanders were killed. Sheppard does his best to argue that on balance, fewer were killed by their presence than would have been the case if they had never been there. A least one of the judges is clearly determined to find them guilty while a second seems far more sympathetic. It's left to Richard Woolsey, who has now joined them, to plead the rest of their case. A lawyer by profession, Richard clearly knows how the game is played and focuses on that third judge. Written by garykmcd

When the power is shut down and most of the inhabitants are locked out of key controls, it is apparent that Atlantis has been taken over by an off-world group, soon identified as Michael and his hybrids. He is after Teyla's newborn child who is key in his quest to gain control of the Pegasus galaxy. While Sheppard and McKay try to get their hands on a jumper to launch an attack, Ronan and others who were taken prisoner by Michael during his initial invasion launch reprisals of their own. When Teyla manages to get away and hide, Michael gives her a simple choice: surrender herself and her child to him or he will use the city's self-destruct mechanism to kill everyone. Written by garykmcd

Radek discovers an alien device that Rodney finds holds serious surprises. Sheppard runs into a reincarnated Acastus Kolya who plans to attack Atlantis. An IOC representative arrives to replace Woosley who receives advice from a mysterious woman. Written by David Foss

Rodney is returning to Earth for his 2 weeks of leave and to attend a colleague's presentation on a scientific breakthrough. He's also managed to work up the gumption to ask Jennifer Keller if she will accompany him and she agrees. On Earth, they're attending a scientific conference hosted by Rodney's rival, Malcolm Tunney, against whom he has been competing for most of his life. When Tunney announces technology to solve global warming, McKay accuses him of stealing his ideas. Tunney decides to give his guests a live demonstration but when he finds he can't turn the devise off, he turns to McKay for help. The crisis also allows McKay and Jennifer to express their true feelings for one another. Written by garykmcd

The team on Atlantis prepare for the worse when they track a Wraith hive ship headed their way. They're surprised to find the Wraith crew in stasis and a message from Todd telling them that Dr. Keller's retrovirus has had an unexpected side effect on them. To protect themselves, they've all entered stasis and returned to Atlantis hoping to get help. Some on the team think they should just leave them in statis and be done with them but a malfunction on the hive ship releases the remaining crew who have been cannibalizing one another for food. Written by garykmcd

When Dr. Jennifer Keller begins to act strangely - she doesn't know her way around the ship and doesn't recognize colleagues - it's pretty obvious that something is very wrong. In fact, her body has been taken over by another woman, Neeva Casol, who describes herself as a thief. She's not quite sure what's happened but she and two others were in the process of stealing ancient relics when she picked up a device and poof!, she suddenly appears in Jennifer's body. She leads Sheppard, McKay and others to the planet in question to see if they can reverse the situation. Jennifer meanwhile is now in Neeva Casol's body and she is about to be executed by the locals. Written by garykmcd

In an alternate universe, Detective John Sheppard is with the Las Vegas Police Department and begins to investigate a strange series of murders. This Sheppard is a bit down on his luck, over-promoted and barely getting by. What Sheppard is dealing with is a Wraith who has made it to Earth and is building a device to send out a signal of some sort. Of course, he has no idea what a Wraith is but a senior member of the Atlantis expedition, Rodney McKay, decides to take Sheppard into their confidence and tell him about the Pegasus galaxy and their fear that the Wraith is trying to send out a signal with Earth's location. While they succeed, they may have opened a rift with other parallel universes. This Dr. McKay, who is cool and smooth, actually visited Atlantis in another dimension once and wonders what may now happen there. Written by garykmcd

In the series finale, the Atlantis team is contacted by none other than their old friend Todd the Wraith, who tells them an underling has marooned him on a planet and taken over the Wraith hive ship. As if that weren't bad enough, the hive ship is now powered by a ZPM and the super-energy source is transforming the craft into an invincible weapon. While those on Atlantis try to destroy the ship, it jumps to hyperspace and has a very clear destination in mind: Earth. Sheppard is recalled home to man their best defense while Teyla, Ronon and McKay find themselves battling the Wraith from within their ship. In the end, Atlantis must travel to Earth for the final battle. Written by garykmcd