Control Ships are massive vessels, apparently built with the sole purpose of ferrying and coordinating a single drone armada. The drones rest on the hull when inactive, and are deployed to destroy any alien technology. Control Ships appear to possess no offensive or defense capabilities, relying solely on its armada for protection. Destiny's main weapon was able to destroy one in only five hits, and it did not appear to have shielding of any kind.
Each Control Ship directly commands its armada, and without it the drones cannot function. In addition, a Control Ship can only control its specific armada, and cannot exert influence over drones of another Control Ship even if it is no longer functional. The drones themselves, however, can act autonomously so long as they are provided with targeting data. The Control Ships can evidently communicate with each other, given their ability to coordinate large-scale blockades. (SGU: "Resurgence", "Deliverance", "Common Descent", "Blockade")
Some time ago, the Ursini awakened a Control Ship and its Berzerker drones, and have been at war with them ever since. When Destiny was attacked by the drones, the Ursini, piloting a Seed ship, rescued them and enlisted their aid in defeating the Control Ship, which would in turn stop the drone armada. Though they were eventually successful in destroying it due to a timely distraction by the Nakai, the Ursini drew the attention of a second Control Ship when they attempted to contact their colony. The Ursini sacrificed themselves to buy Destiny the time it needed to escape. (SGU: "Resurgence", "Deliverance")
Some time later, after the expedition thought they had left drone-controlled space, they were unexpectedly attacked by a drone armada. They escaped, only to be attacked again at the next world they visited. They deduced that the drones had devised a means to track active Stargates through subspace, and switched to shuttle use to counter it. (SGU: "Common Descent")
Not long after, the drones changed strategies, blockading every viable Star used by Destiny to recharge. Unable to fight their way past, Eli Wallace suggested using a blue giant instead, which the drones would be unlikely to blockade since Destiny would never use it normally. The crew was evacuated through the Stargate, hoping that Destiny would finish its recharging before the drones could arrive. However, the planet they gated to, a former Novan colony world, had already been attacked by the drones, and a Control Ship remained in orbit. It sent a few drones to investigate the Stargate activation. After the crew fended off the initial attack, the Control Ship entered the atmosphere in response to the Stargate activating again. (SGU: "Blockade")
Eli Wallace and Dr. Nicholas Rush managed to devise a way to track the Control Ships locations using the signal the ships used to coordinate with each other. Using it they discovered that the ships were blockading all of the planets in the galaxy with Stargates. Desperatly needing supplies, the crew launch an attack on a Control Ship with Destiny's shields modified so they would be more resistant to the drones weapons fire. Destiny dropped out of FTL so close to the Control Ship, it scraped the Control Ship's hull before drones were launched. Destiny damaged the Control Ship with its weapons, so the drones began doing suicide runs, but the crew successfully destroyed the ship before too much damage was done to Destiny. Later, needing ore from meteors, the crew lured the Control Ship blockading the planet they needed to visit into a trap using an Ancient shuttle and a signal that looked like a Stargate dial-out. The shuttle was remote-piloted next to the Control Ship and its engines overloaded, destroying the shuttle and Control Ship. (SGU: "Gauntlet")
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