After Atlantis left to defend Earth from the super-hive, Queen Death rose to power amongst the Wraith and began uniting the Wraith under her control and decimating worlds after feeding on them. Upon their return to Pegasus, the Atlantis expedition learned of Death's rise to power and began opposing her. On the suggestion of a Wraith named Dust, Death decided to capture Doctor Rodney McKay and transform him into a Wraith to put his intellect to good use. (SGA: "Legacy: Homecoming", "The Furies")
In order to trap McKay, the Wraith had a Wraith worshipper travel to the planet of New Athos where the Athosians lived and send out a fake distress call about a Culling. As expected, this drew the First Atlantis Reconnaissance Team to the planet as well as the team of Major Evan Lorne.
Awhile after the team's arrival, three Wraith Darts arrived through the Stargate and were detected by Teyla Emmagan and Kannan who warned the Athosians and the team. In order to buy the Athosians time to get away from the believed Culling, the Atlantis team stood their ground against the Darts. On Sheppard's command, he and Ronon Dex positioned themselves so that the Darts would focus on them and they would dodge the Culling beams while everyone else focused on taking down the Darts. As the first Dart went for Sheppard and Ronon, Teyla fired upon it, but only slightly damaged the craft. The second Dart targeted Teyla, but she was able to dodge its attack and Ronon hit it with his blaster, taking out the Dart's beam generator. The third Dart went into an attack dive on Lorne, but gunfire managed to damage its wing. The Darts focused on the team and capturing McKay, allowing the easier targets of the Athosians to get away. Finally, the Dart with the damaged beam generator did a run on McKay and while he dodged the expected beam, the second Dart was able to position itself perfectly to capture McKay in its Culling beam. At the same time, Ronon was able to severely damage the third Dart while one of Lorne's team did further damage. Having captured McKay, the Darts abandoned the battle and retreated through the Stargate. (SGA: "Legacy: Homecoming")
Following McKay's capture, a Puddle Jumper was sent into orbit where they found no signs of a hive ship and recognized that the event was a raid through the Stargate. Doctor Radek Zelenka was brought in to analyze New Athos' DHD and with the help of Halling and Teyla, was able to narrow the possible planets the Darts could've taken McKay to nine. The team realizes that the Wraith were specifically targeting McKay since they ignored easier targets and focused on him specifically and are left to hope that the Wraith will keep him alive as a result. (SGA: "Legacy: Homecoming")
Over the three days following McKay's kidnapping, Sheppard's team and Zelenka check out the nine possible planets and are finally able to determine that the Darts came from M40-P36, an uninhabited world that's Stargate had dialed only New Athos three times in the previous six months. However, it turns out to be a dead end as the Darts rejoined a hive ship that was waiting in orbit for them and after three days, the hive ship is long gone. After McKay's capture, the Wraith known as Dust is able to turn McKay into a Wraith himself. (SGA: "The Lost")