During their time in the Pegasus galaxy, the Atlantis expedition had commandeered several Wraith Hive ships through various means and used them for their own purposes, albeit usually briefly. These Hive ships have usually been the spoils of war resulting from ship-to-ship space battles.
Atlantis' first hive ship
During the Battle of the Void in 2006, the Daedalus and Orion engaged two Wraith Hive ships, including Nightwind's hive ship, in the massive intergalactic void between the Milky Way and Pegasus galaxies. During this engagement, one Hive was destroyed by the Orion, which too was subsequently destroyed by Nightwind's Hive. It was this Hive that the Daedalus was able to disable and beam over canisters of Dr. Carson Beckett's retrovirus to.
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 taken aboard into the Hive's hanger where it remain during the Hive's voyage back to Atlantis.
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 and 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 got to the point were they could 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 escaped in a Puddle Jumper shortly before it was destroyed by the Wraith controlled Hive, which later retrieved the transformed Wraith from the planet's surface. After the Daedalus' hyperdrive was repaired, the ship was sent to retrieve the team in the Puddle Jumper and return them to Atlantis. (SGA: "No Man's Land", "Misbegotten")
Atlantis' second hive ship
The Atlantis expedition later received a signal from Todd's tracking device and followed it to a derelict Hive ship that showed signs of being attacked by another Hive. Dr. Rodney McKay accessed the ship's records and found that it had been heading to a secret Wraith facility that was supposedly instrumental in defeating the Lanteans. Teyla Emmagan, using her latent Wraith abilities combined with that of her unborn son, managed to take the Hive to hyperspace towards the location of the facility.
When they reached the planet, Lt. Colonel John Sheppard and his team took a Puddle Jumper down and infiltrated the facility while the Hive ship remained in orbit with Teyla and Major Evan Lorne. They freed Todd, who told them that it was meant for cloning and that he had intended to power it using Zero Point Modules captured at the Battle of Asuras. The team was then attacked and captured except for Todd, who flew a Wraith Dart to the Hive. The exhausted Hive queen running the cloning process was about to feed on McKay when Teyla controlled her mind and used her to free them. While the team evacuated in the Jumper, another Hive dropped out of hyperspace and attacked their own vessel. Todd returned fire until they escaped and crashed the ship into the facility, destroying it. (SGA: "Spoils of War")
Atlantis' third hive ship
This Hive Ship shows up over Atlantis transmitting a distress call, Lt. Colonel John Sheppard's team discovers that its crew has been stricken with a disease they helped create. After being tracked for several days, it exited hyperspace over New Lantea and transmitted a file to Atlantis, which has taken precautionary defensive measures including raising the cloak. After seeing the highly corrupted video file, Lt. Colonel John Sheppard and his team are sent to try and make contact with the Hive via cloaked Puddle Jumper.
However, as they try to establish radio contact, Dr. Rodney McKay discovers that there are no life-signs aboard. Curious as to how the ship flew itself to Atlantis, the team lands in the ship's Dart bay. Upon securing the - apparently abandoned - ship and making their way to the bridge, they discover that the Wraith crew is in stasis, with all hands stricken with a disease caused in part by Dr. Jennifer Keller's gene therapy. The team also notices a series of power fluctuations occurring on the ship, wreaking havoc on the ship's systems.
The team later noticed that the ship's schematics - which they were using to navigate through the ship - were no longer accurate, as new walls were forming and other ones are being destroyed... literally melting away. As such, the team attempted to leave the ship, as it was experiencing an increasing amount of power fluctuations and systems failure, and the team didn't want to take the chance that any more Wraith would inadvertently come out of hibernation due to a subroutine in the ship that automatically revives them during power failures. However, a possible escape route to the dart bay had been blocked by a newly formed wall, leaving only one other passage... a passage that has been completely destroyed, leaving a huge gap in the ship, and the team stranded.
McKay then comes up with a theory as to the ship's problems: Because Wraith ships are organic and repair themselves, it is possible that the ship is repairing itself incorrectly. However, because the problems with the ship are too serious and lacking the knowledge to properly fix it, McKay persuades Sheppard to revive Todd. It is Todd who discovers the reason for the ship's problems: during hibernation, fluids are exchanged between the Hive Ship and the occupant of the hibernation pod. Because the Wraith in the pods were infected with the virus, the ship became infected with it as well, leading to the power failures and malfunctions.
As the ship began to loose integrity, a massive stress point spanning the entire width of the ship finally fails, splitting the ship in half moments after the teams fighting the Wraith make it to the front portion of the ship. As the back half remains in orbit, the forward half containing the Atlantis team begins to lose its orbit, and descends into the atmosphere of New Lantea. With no hope of stopping the ship in time, the team re-enlists the help of Todd. As he makes his way back to the bridge, he quickly gains control of the ship, firing the forward thrusters with all of the remaining power. However, the ship is rapidly descending. Todd then manages to level out the ship moments before it slams into the oceans of New Lantea, sending a huge wave out in all directions. Atlantis sends out rescue teams that are able to reach the team who were knocked out in the crash and remove them from the ship which then sinks in the ocean. (SGA: "Infection")
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