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After Destiny had dropped out of FTL a Control Ship dropped out of hyperspace and launched several Berzerker drones against Destiny, which began shooting at the ship. The crew of Destiny destroyed the drones and the one they had captured in case that was how they were tracking them, but the Control Ship followed them as they tried to escape at sublight speed. (SGU: "Common Descent")
After Destiny automatically shut down its sublight engines to prevent them from burning out, the Control Ship caught up and launched more drones at it. Destiny fought off the attack, taking minimal damage in the process and by diverting all power to the shields, managed to hold out until the jump countdown ran out and they escaped to FTL, destroying a few drones that were too close. (SGU: "Common Descent")
After the attack, the expedition found the Novus colony and established relations with the people there, getting needed food and water supplies and lime for the CO2 scrubbers. The drones detected the Stargate activity and attacked both the colony and Destiny. Some of the settlers escaped to Destiny through the Stargate, but weapons fire from a drone severely damaged the Stargate, rendering it inoperable before it was shot down by MSgt. Ronald Greer. After destroying all technology in the area, the drones left. Meanwhile, Destiny escaped to FTL, taking minor damage. (SGU: "Common Descent")
Afterwards, Lt. Matthew Scott, Chloe Armstrong, Camile Wray, MSgt. Ronald Greer and Eli Wallace were stranded on the Novus colony with the survivors of the attack with no way back to Destiny and no way for the crew to know it was safe for them to return for them in the shuttle. Eventually Eli managed to send a Morse code signal through the Stargate's connection to Destiny and the survivors of the attack were rescued and they headed to Novus to check the planet out. (SGU: "Common Descent")