- "Currently, Stargate Command has no vessels capable of engaging the Hive Ships before they reach Earth. They cannot be allowed to get that far."
- —Elizabeth Weir
- "All we want is the retrovirus. It is the key to ending a civil war that could go on for centuries."
- —Nightwind to Elizabeth Weir
In 2006, a Wraith faction represented by Michael Kenmore proposed an alliance with the Atlantis expedition. Earlier that year, Dr. Carson Beckett's Iratus bug retrovirus was tested on Michael Kenmore, successfully turning him into a human for a brief time before he ultimately started reverting back into a wraith and later rejoined them, carrying with him the knowledge that Atlantis still existed. In exchange for Dr. Beckett's retrovirus (which Michael now sought to use in order to turn the Wraith of rival Hive Ships into humans to feed upon), Michael gave the Atlantis Expedition valuable technical information detailing Wraith weapons and defenses. This alliance was, however, turbulent given the mutual distrust felt among both parties, and the fact that Michael could transmit the location of Atlantis to the other Wraith in the galaxy at any time. The Atlantis Expedition's distrust would ultimately be justified, however, as it was later discovered the Wraith were actually using the alliance as a pretense to gather two key pieces of information: the Aurora mission report (in order determine out how to upgrade Wraith hyperdrives) and the location of Earth. This was accomplished by means of a spyware computer virus planted into the Atlantis database by the wraith, hidden in the Hive Ship technical data which had been given to the expedition as per the terms of the alliance.
In the final days of the alliance (just before the full nature of Michael's deception was made apparent) the Daedalus and Michael's Hive ship were sent on a joint mission to attack an enemy Hive with a gaseous version of the retrovirus, as to prove the gas' effectiveness. Emerging from hyperspace at the predetermined coordinates, the Daedalus, however, fell victim to a surprise attack by both Michael's Hive and the "enemy" Hive, which immediately opened fire on the Daedalus the moment the ship came out of hyperspace. In an attempt to resist the two Hives, the Daedalus opened fire using all main Railguns batteries and raised shields. A squadron of four F-302 fighter-interceptors (including one piloted by Lt. Colonel John Sheppard) was promptly launched to intercept the incoming wave of Wraith Darts. Concurrently, Ronon Dex and Dr. Rodney McKay, who were on the "allied" Hive ship (as to oversee the deployment of the retrovirus gas on an "enemy" Hive ship) were captured and imprisoned in adjoining cocoons, revealing to them Michael's true intentions. Before the Wraith abruptly withdrew from the engagement and entered hyperspace (having been in the heat of battle just moments prior), Colonel Sheppard, who had been attempting to disable the Hives' hyperdrives, used his F-302 to latch onto the hull of one of the Hive ships before it took off into hyperspace. After recalling all fighters and scanning the wreckage for survivors, the Daedalus set a course back to Atlantis. (SGA: "Michael", "Allies")
Back in Atlantis, after discovering the Wraiths' deception and that they were headed for Earth, Dr. Radek Zelenka calculated where the Hive ships would need to drop out of hyperspace to regenerate their hulls for the last time before making the final jump to Earth. Dr. Elizabeth Weir then dispatched the Daedalus (which was still being repaired for the moderate damage it had incurred during the previous engagement) and the newly acquired Aurora-class battleship Orion to the location - in the massive void between the Milky Way and Pegasus galaxies - to stop the Hives. Colonel Steven Caldwell expressed his concern with the strategy, believing it could very well be a suicide mission. Weir acknowledged this fact, but ultimately (and reluctantly) knew it was the only option available.
Meanwhile on one of the Hive ships bound for Earth, Michael Kenmore discovered that his life was in danger as the ship's Queen no longer trusted him - believing he was an abomination after what the Atlantis Expedition had turned him into in their experiments. McKay and Ronon meanwhile managed to escape from captivity and attempted to sabotage the Hive ship that they were in. Knowing he could no longer remain on the ship or trust his fellow Wraith, Micheal managed to contact Sheppard and instructed him to attack the Hive (both of which had already arrived in the intergalactic void) with what little ordinance remained in his F-302. In the attack, Sheppard damaged the hyperdrive of one of the ships. However, hundreds of Darts were launch in response which, after critically damaging the F-302, held position around both hive ships. Sheppard was then taken aboard the Hive and questioned by the ship's Queen. (SGA: "No Man's Land")
- "I was coordinating a strike against the Hive Ships when you recalled me... With everything we've got."
- —Elizabeth Weir
On the bridge of the ever-approaching Daedalus, Colonel Steven Caldwell prepared the ship for battle, ordering Captain Dave Kleinman to rig all operable missile launch tubes to fire Mark III tactical warheads the second the Daedalus exited hyperspace; hoping to destroy the Hive ships before they had time to react. Furthermore, all non-essential power was rerouted to the shields in order to ensure power levels for a longer period.
As the Daedalus emerged from hyperspace at the coordinates, dozens of missiles were immediately launched, all of which raced toward the closest Hive ship at various trajectories. However, hundreds of Wraith Darts were detected in proximity to both Hive ships. As the onslaught of missiles grew closer, these darts moved to intercept, with the closest of which careening into the missiles as to prevent them from reaching the Hive. In the Daedalus' opening salvo, one of the Hive ships was severely damaged in a brilliant blue explosion, but not completely destroy as all but one of the warheads were intercepted by the swarms of Darts.
Moments after the Daedalus' initial attack and both Hive ships opened fire in retaliation, the Orion, commanded by Major Evan Lorne, arrived. However, as the ship had been rushed into battle, Dr. Radek Zelenka had difficulty simultaneously transferring power from the shields to the Drone weapons. When the problem was corrected, the Orion fired a massive salvo of drones. Upon leaving the Orion, the onslaught of projectiles raced toward the nearest Hive ship, weaving in and out of the waves of approaching Darts in order to reach their target. After just a few seconds, this massive salvo bombarded the hull of the Hive ship, blasting thousands of deadly holes as the lethal and resilient weapons propelled themselves into and out of the craft several times. This brutal attack was more than enough to completely destroy one of the Hive ships. However, in order for that salvo to be launched, the Orion's powerful shields were sacrificed, leaving the warship vulnerable. The remaining Hive ship then shifted its attack toward the Orion, the hull of which began taking multiple hits. Unable to fire again and hull breaches occurring across the ship, destruction was inevitable. As the Daedalus was too far out to intercept, Orion's crew was beamed over to the Daedalus by the request of Lorne. Just moments later, the Orion finally succumbed to the intense firepower of the Hive and was destroyed in a massive, fiery explosion.
Meanwhile, Michael Kenmore, Lt. Colonel John Sheppard, Ronon Dex, and Dr. Rodney McKay managed to escape from the remaining Hive ship in a Wraith scout ship and were beamed directly onto the bridge of the Daedalus moments after the Hive opened fire on them. Before their departure, Michael managed to deactivated the ship's jamming code, which would enable them to beam a Nuclear warhead into the Hive. However, none remained as all Mark IIIs were fired in the Daedalus' opening salvo.
As the Hive ship then began to launch a wave of Darts against the Daedalus, the Daedalus brought all Railguns to bear on the Hive's main Dart bays and every ounce of power was channeled to the forward shield. In the barrage of railgun fire that followed, these projectiles impacted the Hive's Dart bays at incredible speeds, completely destroying the incoming darts moments after they launched. The concentrated fire on the bays also created a number of secondary explosions inside the ship which stopped the Hive from firing and left the entrance to the bay in a fiery cloud. However, in the process, the Daedalus' shields became completely depleted and the ship sustained several direct hull impacts, exposing several interior sections directly to space. The last blast the Daedalus sustained took out life support and left the back-up systems unresponsive. With the only source of breathable air in light years being aboard the Hive ship, the Daedalus beamed over the retrovirus gas in order to convert the Wraith on the ship into Humans, therein eliminating the Wraith threat and providing a lifeboat for the Daedalus' crew. Once the gas had a chance to "run its course" (a process which takes several hours), a small team of Marines was beamed over to the Hive to secure the ship. (SGA: "No Man's Land")
- "We're out of food and water and we haven't slept in days but, yeah, we made it."
- —John Sheppard
Many Wraith died in the conversion process and some even fed on each other. However, the surviving 200 Wraith were transformed into humans and were placed in stasis chambers aboard the Hive ship, which was commandeered by the Atlantis expedition. After the battle's conclusion, the Hive ship was briefly taken to Atlantis. As the Daedalus had sustained heavy damage to many systems, including its hyperdrive, the ship was towed through hyperspace during the Hive's voyage back to Atlantis. (SGA: "No Man's Land", "Misbegotten")
Due to the strain on the Hive ship's energy reserves caused by keeping 200 human-converted Wraith in stasis, a more permanent solution was devised; The humans would be taken to M8G-352 where they would be placed under quarantine. However, after discovering that they were in fact Wraith and not humans, the captured Wraiths started to transform again and reverted to the point were they could telepathically contact a Wraith-controlled Hive ship to rescue them. As to not let them, once again, fall into the hands of the Wraith, the Atlantis expedition's Hive opened fire on the planet shortly after the Wraith-controlled Hive exited hyperspace. The team aboard Atlantis' hive ship escaped in a Puddle Jumper shortly before it was destroyed by the Wraith controlled Hive, which later retrieved any surviving transformed Wraith from the planet's surface, including Michael. After the Daedalus' hyperdrive was repaired, the ship was sent to retrieve the team in the Puddle Jumper and return them to Atlantis. (SGA: "Misbegotten")
Although the Wraith suffered heavy losses with the destruction of a Hive ship, Michael still survived the battle and was picked up by the other Hive ship. It is unknown if any other Human-form Wraith survived, but if they did, they were likely killed by the Wraith as Michael ultimately had to flee for his life. (SGA: "No Man's Land")