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Destiny and her crew come upon an Ancient seed ship crewed by the Ursini soon after Doctor Nicholas Rush finds Destiny's bridge and the crew are forced to leave behind Colonel David Telford when the seed ship starts draining power from Destiny and Rush is forced to undock the two ships. Telford and the Ursini end up forming an alliance and repair the seed ship and head out to catch up with Destiny. Later, the ship comes across a damaged Ursini spaceship from an attack by the drones, but were unaware of what caused the damage. A month after finding the seed ship, Destiny picks up an energy signal and the crew heads to check it out and finds a graveyard from an attack by the drones on the Ursini.
- Main article: Drone attack on Destiny
While Sergeant Ronald Greer, Lieutenant Matthew Scott and Doctor Adam Brody investigated one of the wrecked Ursini spaceships, they woke up drones that were dormant in the graveyard. At the same time, the crew learned from a simulation of the battle that all the drones weren't gone and recalled the shuttle and battled the drones. The ship managed to fight the attack off long enough for the shuttle to land, but the damage Destiny took in the battle caused the FTL drive to go down and the ship is unable to escape. As the crew tries to figure out what to do, Telford and the Ursini arrive in the seed ship and lead Destiny through a nearby star to recharge, destroying the drones following them. The crew and the Ursini form an alliance to destroy the drones Control Ship in exchange for the Ursini allowing Destiny to use the seed ship's power reserves to dial Earth when its over. The Ursini betray the deal and during the couple FTL jump, take Destiny straight to the Control Ship. Destiny is no match for all the drones until Chloe Armstrong suummons three Nakai motherships which draw off some of the drones. Thanks to the distraction and Eli Wallace and Nicholas Rush jamming the control signal for the drones, Destiny is able to destroy the Control Ship. Two Nakai motherships are destroyed in the battle while the last is severely damaged. Destiny is also severely damaged and while its FTL drive is fixed not long afterwards, five of the shield relays are burnt out and the ship can't jump until they are bypassed. The Ursini's attempt to contact their colony draws a second Control Ship to the site of the battle before Destiny is repaired and after repairing their hyperdrive, the Nakai leave, leaving Destiny to face the second wave on its own. Using information taken from a captured drone, Eli and Rush try to make the first wave of drones attack the second, but don't have enough time so the Ursini launch a suicide attack on the Control Ship, drawing off the drones. The seed ship is destroyed, but it buys Eli and Rush the time they need and the two waves of drones battle it out. With the drones distracted, the shuttle with Scott and Chloe on board is able to dock and Brody and Dale Volker are able to finish the repairs to the shields. The shields return, but only at five percent which the crew knows may not be enough to survive FTL, but have no choice and Destiny jumps to FTL. The ship survives the jump, but takes severe damage in the battle. (SGU: "Resurgence", "Deliverance")
- Main article: Second Drone attack on Destiny
While Destiny is trying to resupply, the drones detect the ship using the Stargate and attack. At first there's only six drones which are easily shot down, but more arrive including an entire Control Ship so the crew head away from the Control Ship at maximum sublight speeds for as long as the ship can handle it so they can stay out of range until the ship can jump to FTL. Fearing that the drone captured in the initial encounter with the drones is being used to track the ship, its jetisoned and then destroyed. Destiny's sublight engines eventually shut off, but it ran for long enough and got them far enough away that the drones didn't catch up until just before the ship jumps. As the drones swarm the ship, Destiny jumps, destroying a few drones that were nearby. When Destiny sends a team to a nearby Novus colony, the drones detect the Stargate activation on both the ship and at the colony and drones attack both. Targeting the technology of the colony, the drones hit the Stargate, damaging it while the colonists were evacuating to Destiny. One was shot down and the rest left when all of the colony's technology was destroyed. Taking damage and no longer able to dial the colony, Destiny was forced to flee to FTL. The remaining colonists, Scott, Greer, Eli and Camile Wray end up trapped on the colony until Eli manages to use the Stargate's connection to Destiny to send a Morse Code message saying it was safe to come and pick them up. (SGU: "Common Descent")
- Main article: Drone Blockade of Destiny
Discovering Destiny's need to recharge at red dwarves, the drones began blockading all of the stars in and off of Destiny's path of that type so Destiny would be forced to face them in battle to recharge and would be vunerable due to the low level of power it would posses at the time. The crew of Destiny discovered this when they went to recharge and found the star blockaded by drones and a Control Ship. An attempt was made to evade the drones and recharge as the drones couldn't follow the ship into the star, but the drones simply moved to block the ship as it did this. The drones opened fire on Destiny, but the ship's shields absorbed it. Deciding not to fight when they could simply find another star and thanks to an aerobraking maneuver time runs out soon afterwards, the crew jump to FTL and head for another star. Rush decides to take Destiny off its path figuring the drones wouldn't be there, but just to be safe, Destiny drops out of FTL away from the next star and elapses the needed time in case drones are waiting. Just after the countdown elapses, the drones arrive and low on power, Destiny is forced to jump again. Realizing that its a blockade and that its likely on every star in the path, Eli come up with a plan to reharge inside a blue giant instead, a star that the drones would never expect the ship to fly into. In order for the crew to be safe, they are sent through the Stargate to a nearby planet as Eli, Rush and Doctor Lisa Park stay behind to pilot Destiny in the Ancient environmental suits, knwoing the drones will likely be drawn by the Stargate activation, but hopefully not before they leave. Unfortunately the planet they land on has been attacked by drones before and at least two drones remain on the planet. Drawn by the Stargate activation and locking on to the crew's radio signals, the drones attack the search teams Colonel Everett Young sends out into the city. One is drawn away when Morrison tries to dial the Stargate while the other one attacks the teams led by Scott and Greer. Scott, Greer and Colonel Young manage to shoot down that drone while the other one is drawn in by a radio call from Lieutenant Vanessa James and is destroyed by a shot from a Lucian Alliance rocket launcher by Varro. Destiny is successfully recharged although Park is flash-blinded, but on the planet a Control Ship arrives and the crew is forced to evacuate to Destiny ten minutes early. (SGU: "Blockade")
- Main article: Destiny attack on Drones
Isolating the subspace signals the drones use to communicate with each other and plugging that into Destiny's long-range sensors, the crew learn that the drones are blockading every planet with a Stargate between their position and the end of the galaxy. Needing to resupply, the crew decide to attack the drones at a planet where a Control Ship is blockading using the information they gained from the drone they captured during the first battle to modulate the ship's shields so they are resistant to the drones weapons. Destiny drops out of FTL right on top of the Control Ship and engages in battle with it, managing to damage it with Destiny's main weapon and resist the drones weapons until they launch suicide attacks which the modulated shields aren't able to defend against. Eventually Destiny successfully destroys the Control Ship, but takes damage and the crew get very little food supplies from the planet. Eventually Eli comes up with a plan to enter the ship's stasis pods to skip the rest of the galaxy, but in order to fix eight of the pods, the crew needs palladium hydride which is on a planet blockaded by a Control Ship. As part of a plan, Destiny launches one of its shuttles with its shields modulated and broadcasting the same signal an active Stargate broadcasts, drawing in the Control Ship. This allows a team to travel to the planet through the Stargate to retireve the needed minerals and the shuttle's engines are overloaded right next to the Control Ship, destroying it without Destiny taking any damage. (SGU: "Gauntlet")
Destiny is able to begin its trip out of the galaxy with all but Eli in stasis. One pod is too badly damaged to fix in time and he remains out to try to fix it within a two week timeframe. If he is unsuccessful, he will die. (SGU: "Gauntlet")