Following Atlantis' return to the Pegasus Galaxy after six months on Earth, the expedition learns of the rise of a new powerful Wraith Queen, Queen Death who is uniting all of the Wraith under her control and destroying human worlds. A short time after the Wraith defeat at the Battle of Levanna, Queen Death has a Wraith worshipper send a false distress call to Atlantis that draws the First Atlantis Reconnaissance Team to New Athos where she launches a raid through the Stargate with three Wraith Darts to kidnap Doctor Rodney McKay. Queen Death's forces succeed in capturing McKay who is then transformed into a Wraith to better suit Queen Death's purposes.
Following the kidnapping of McKay, the Atlantis expedition sets out to find him, locating the planet the raid was launched from only to find the Wraith long gone. Without any other clues, the expedition turns to the Genii and the Wraith Commander Guide as alternative sources of intelligence. Guide eventually contacts the expedition with the location of a planet that Queen Death's hive ship Bright Venture will soon be orbiting with McKay in the forward laboratory section. Guide informs the expedition that this will be a perfect time to strike as Bright Venture will be in a state of dormancy for four to five hours while the ship consumes the raw materials it will need to repair itself and expand and will thus be vulnerable to attack. The decision is made to send the George Hammond to the coordinates to rescue McKay and hopefully destroy Bright Venture and with it, Queen Death. (SGA: "Legacy: Homecoming", "The Lost")
Approaching the coordinates, Colonel Samantha Carter warns Lt. Colonel John Sheppard, Teyla Emmagan and Ronon Dex that as soon as the Wraith detect the George Hammond, they will likely start waking up Bright Venture which will eventually restore the hive ship's defensive systems, including its jamming code. While the George Hammond could possibly disable the hive ship's defensive systems in that case, if things start to go bad, they will either have to pull the team out and jump to hyperspace or leave and the team will have to find their own way out. The team accepts this and as soon as the George Hammond emerges from hyperspace, they are beamed into what they guess is the laboratory section of the ship.
The team begins making their way through the ship, using a life signs detector to keep a watch out for Wraith and to help them choose their path. Reaching an empty laboratory, Teyla attempts to use her abilities to access the ship's database to help find McKay, but states her belief that while the ship is dormant, the main databanks may not be accessible. After Teyla ultimately determines that she can't activate the console and thus can't get McKay's location from it, the team leaves the room and continues their search. Their search continues fruitlessly until they detect a Wraith through the life signs detector. Ronon is able to quickly kill it with his particle magnum, but Teyla is unable to determine if he was able to raise an alarm due to there being too much alarm and confusion amongst the Wraith due to the appearance of the George Hammond and their efforts to wake the ship up. After a while more of searching without luck, Teyla decides to have them capture a Wraith so she can get McKay's location from his mind instead as the Wraith will know they are there soon enough if they don't already and they are limited on time. The team uses the life signs detector to track down a lone Wraith scientist who Sheppard shoots through the shoulder with his FN P90 Personal Defense Weapon and Ronon pins to the wall. After the Wraith is pinned, Teyla approaches and communicates with him telepathically, using her training from Guide to command the Wraith to tell her where McKay is. Thanks to Guide's training and the power of her mind which is equivalent to that of a Wraith Queen, Teyla is able to get the Wraith to direct them to the laboratory that McKay is in which is close by. She then uses Ronon's particle magnum to stun the Wraith rather than kill him as Sheppard, Ronon and the Wraith were expecting. Making their way to the lab, the team comes under fire from Wraith alerted to their presence.
At the same time, McKay, now the Wraith Quicksilver and the Wraith scientist Dust are warned of the attack by the ship's alarms as the Wraith try to power Bright Venture back up and launch the Wraith Darts to respond to the threat from the George Hammond. As Sheppard's team approaches the lab, Quicksilver and Dust hear the sound of the team's weapons and Wraith stunner fire, causing Dust to retrieve a Wraith handblaster he has stored in the lab for emergencies. As Ronon covers them, Sheppard and Teyla blow in the door to the lab and enter the room where Sheppard calls out for McKay and Ronon warns them to hurry as he won't be able to hold the Wraith off for long. As Sheppard calls for McKay, Dust darts out from hiding and opens fire on Sheppard and Teyla with his stunner, narrowly missing Teyla and catching their attention. In response to Dust's attack, Sheppard kills him with fire from his P90. Not recognizing his friends and enraged by the death of the Wraith he believes is his brother, Quicksilver grabs Dust's stunner and shoots Sheppard with it six times, leaving him unconscious and bleeding from the ears as Quicksilver fires at Teyla who takes cover from his attack.
At the same time, as the Wraith wake Bright Venture up and launch their Darts, the George Hammond attacks the hive ship with her railguns, traveling along the lateral surface of the ship, firing the whole time before turning to make a dorsal pass. During the attack, the George Hammond is peppered by fire from the Darts which part before the Tau'ri warship when it turns then follows to attack from the aft. The fire from the George Hammond causes the hive ship massive damage, depressurizing several sections. As Carter calls for a status report from Sheppard, she is warned that the George Hammond's aft shield is at forty percent, the ship having taken apparent physical damage to the starboard ventral shield emitter. As the George Hammond dives and rotates 280 degrees to avoid another flight of Darts, Bright Venture starts to power up with all systems starting to come back online. Suddenly, the damaged shield emitter blows, causing the George Hammond to lose the entire rear shield and Carter orders power cut to the damaged sections. With her ship vulnerable and the hive ship nearly ready to block their ability to beam the team out, Carter calls to Sheppard that they have to beam them out now or leave them behind.
Hearing the radio call and under heavy attack from Wraith warriors, Ronon warns Carter that Sheppard is down and she alerts him to the fact that she can't give them anymore time: the George Hammond is about to open a hyperspace window and can either beam them out now, or they will have to find their own way home. Hearing this, Ronon enters the room to find Sheppard unconscious, Teyla taking cover and McKay a Wraith that is attacking them with a stunner causing the horrified Ronon to remember their experiments with the Iratus bug retrovirus that turned Wraith into humans. As Carter warns that the George Hammond's hyperspace window is open and Ronon has about ten seconds to make a decision, Teyla tries to call out to McKay to no avail. As Carter calls upon Ronon to make the call about whether or not to stay, he realizes that even if they could stun McKay, Sheppard is unconscious and without him, they don't have someone who could pilot them off the ship in a Wraith Dart. As well, the room is surrounded and they'd never escape it alive and Sheppard needs medical help. Reluctantly, Ronon orders Carter to beam them out and once they are on board the George Hammond, Carter orders her ship into hyperspace, the mission a failure. (SGA: "The Lost")
Following the battle, Sheppard is taken to the infirmary where he is monitored due to the effects of being stunned so many times, but it is determined that he will be alright. The George Hammond's engineers determine that the shield emitter is completely blown away and they will need a full machine shop to fix it. While the ship has the necessary parts and the repair can be done on Atlantis, it will take a week to do. Carter also speculates that the George Hammond crippled Bright Venture fairly well, believing that the attack took out Bright Venture's hyperdrive, forward weapons systems and caused major structural damage that will take ship out of commission for months. However, as Queen Death commands a big alliance, she will likely change flag ships. The Atlantis expedition also has to deal with the consequences of McKay being a Wraith, namely the amount of knowledge he has about Atlantis and its systems and the many backdoors he has placed within the city's systems that McKay can use to leave them defenseless. (SGA: "The Lost")
Despite the belief that Bright Venture will be crippled for months, Queen Death calls in the scientists of half a dozen other hive ships and they are able to repair Bright Venture within weeks. Having been previously unaware of McKay's transformation into Quicksilver, Guide gets Queen Death to allow Ember to take Dust's place in guiding Quicksilver to helping them defeat Atlantis. (SGA: "Allegiance")