Periodically, Destiny needs to recharge in stars, preferably red dwarfs as the damage to the ship causes the ship to only be able to hold forty percent power. The drones learned of the weakness and started blockading all stars in Destiny's path that met the criteria for recharge so the ship would have to face them in battle if it wanted to recharge.
Needing a recharge, Destiny set course for a star, using an Aerobraking maneuver around a gas giant to travel to the star. There, the crew found a Control Ship blockading it and engaged it and its drones in battle in an attempt to get around them and reach the star, which the drones couldn't follow them into. The drones simply moved to block their path and unable to take a battle with the drones and having elapsed enough time because of the aerobraking maneuver, the crew escapes to FTL with minimal damage rather than continue to fight.
Still needing to recharge, the crew sets a course for a star outside of Destiny's projected path to recharge hoping not to find the drones there. In order to be sure they will be able to jump to FTL if necessary, the crew drops out early and waits the full time for the drives to cool down. As they reach the end of the time limit, the drones attack again and Destiny jumps again rather than try to fight.
Running low on power and needing desperately to recharge, Eli Wallace comes up with a risky plan to recharge inside of a blue giant rather than a red dwarf, a plan which requires most of the crew to evacuate the ship while he and Dr. Nicholas Rush stay behind and use the Ancient environmental suits to manually pilot the ship through the star. The crew evacuates to the only planet in range, a Novus colony which appears to have been abandoned. They know the Stargate being used will draw the drones, but hope to be gone before they can get there. On the planet, they scavenge for supplies and Dr. Morrison learns from a newspaper that the planet was attacked by drones. The paper also indicates the gate's location, having been moved from a more advanced to a less advanced city, allowed a majority of the population to escape.
While searching the city for supplies, one of the drones that remained on the planet locked in on the radio signals and pin down the search teams. Another drone soon arrives to assist but Morrison's attempt to dial the gate draws it away. The first drone was destroyed by Colonel Young, Lt. Matthew Scott, MSgt. Ronald Greer, while Lt. Vanessa James and Varro coordinated the destruction of the second. Upon hearing what turns out to be a Control Ship approach, the crew return to Destiny ten minutes early before the ship can launch it's drones.
Eli's plan works and Destiny is recharged, but Dr. Lisa Park is flash-blinded trying to save plants from the Destiny garden. While the plan is successful, it is not likely to work again. Also, the drones started blockading all planets with Stargates on Destiny's path. (SGU: "Blockade", "Gauntlet")