While following a tip on the possible location of a Zero Point Module, Lt. Colonel John Sheppard and his team were captured by Aiden Ford's gang, with the purpose of formulating a plan to destroy a Wraith Hive ship using C-4 explosives they stole back from the Genii. Both teams managed to repair a damaged Wraith Dart and used the craft to gain access to a Hive ship. However, as they entered the Hive, they soon became discovered and were easily outnumbered. They were all subsequently stunned and sent to a holding cell.
Meanwhile, Dr. Elizabeth Weir sent Major Evan Lorne and his team to find Sheppard's team. However, with such a wide number of planets in the Pegasus galaxy, the chances of finding them were slim at best. Dr. Rodney McKay was eventually able to escape Ford's compound by overpowering the guards whilst under the influence of a massive dose of the Wraith enzyme. He came back to Atlantis, where he went through withdrawal. After finally recovering, he gave the coordinates of the Hive ship at a planet named Edowin gotten from Ford's intelligence on where it was heading to. However, the Hive has allied with another Hive ship to cull this world.
The Daedalus was quickly dispatched to the planet and sent Lorne and McKay, via cloaked Puddle Jumper, to rescue Sheppard and Ford's team. They attempted to radio Sheppard, but received no signal, so they assumed they were killed. They returned to the Daedalus, which intended to destroy the ships before they could cull the humans on the planet below. (ATL: "The Lost Boys", "The Hive")
- "We need to take those ships out before they start culling."
- —Steven Caldwell
Colonel Steven Caldwell intended to beam Nuclear warheads on board the Wraith Hive ships, but they managed to deploy Jamming codes, preventing such action. However, as the possibility existed that the Wraith were able to discover that Atlantis still existed from Lt. Colonel John Sheppard's and Aiden Ford's team, Daedalus had to destroy the enemy Hives. While the Daedalus attacked the Hives with Railguns, Sheppard, Ford, Teyla Emmagan and Ronon Dex managed to escape from their captivity, but Ford remained behind to hold the Wraith off.
Sheppard managed to acquire a Wraith Dart and beamed Teyla and Ronon up into it. After leaving the Hive, the other Darts were heading towards Edowin, so Sheppard decided to open fire on the neighboring Hive. This started a battle between two squadrons of Darts. Eventually, the two Hives fired on each other, until both of them were destroyed, destroying everything within a 15,000 meter radius, including all the Darts. After the Hives destruction, the Daedalus detected nothing but debris and assumed Sheppard was killed in the blast. (ATL: "The Hive")
Lt. Colonel John Sheppard managed to fly the Wraith Dart to Edowin's Spacegate and dialed an address where he could land safely as he realized what was going to happen and that he'd never make it to the Daedalus in time. He Gated to another planet, dropped off Teyla Emmagan and Ronon Dex and abandoned the Dart, before gating back to Atlantis. This battle along with the lack of food in the galaxy started the Wraith civil war. (ATL: "The Hive")