The Mutiny on the Destiny was an event aboard Destiny in 2009, wherein the civilian personnel staged a takeover of the ship in order to force Colonel Everett Young into submitting to civilian authority. During the mutiny, however, Destiny also became under attack from an alien race.
Shortly after Dr. Nicholas Rush returned to Destiny following his abandonment on the Gravel pit planet, he hatched a plan with Camile Wray to take control of the ship. Using a vacant Research lab as a temporary command center, he arranged to transfer all command functions from the Control interface room. The need to destroy a Nakai fighter which was latched to the hull, and thus giving away their position to the Nakai, gave him the opportunity to implement his plan. (SGU: "Divided")
In the midst of transferring control, Dr. Nicholas Rush's actions accidentally disabled the Docking clamps for the Ancient shuttle. Colonel Everett Young and Lt. Matthew Scott were aboard, and would be killed if the shuttle was not docked when the ship returned to FTL. Though resistant to the idea of ending his plan before it even got started, Rush ultimately relented under pressure from Chloe Armstrong and Camile Wray, stopping the transfer to allow docking.
Despite cutting off the transfer early, Rush still managed to take control of almost every major system. He sealed every corridor leading to the Gate room, Mess hall, and Hydroponics lab, stranding the military on the opposite side with no food and water. However, Young had control of life support, though the point is moot as he could not leverage this against Rush since their side would die of dehydration in the same time it would take for the other to suffocate.
Rush arranged to give the military a small supply of food and water in exchange for Eli Wallace, both to keep Eli from restoring control of the ship and because he needed Eli's help in transferring power to the shields. Young uses this as a distraction to go outside the ship through one of the hull breaches, entering on the civilians' side through another one. Once there, MSgt. Ronald Greer and Young split up. Young went to find Rush, while Greer went to open up the doors to let the rest of the Marines through. On his way to let the Marines through, Greer knocked out three civilians. Once inside, the Marines worked to the mess hall, where Lt. Vanessa James subdued another civilian who was uncooperative. They used the mess hall as a staging point, and sent other marines to round up the remaining civilians.
Meanwhile, Rush reveals that he has been using Wray for his own purposes: there is a Tracking implant in his chest, surgically implanted by the Nakai, and he needs Eli's help to resist the upcoming assault. Eli helps transfer as much shield power as possible while Young subdues the civilians.
Three Nakai motherships drop out of Hyperspace near Destiny and open fire, trying to collapse the shields. Wray confronts Rush about this, realizing that he has used her plan to protect himself. Rush points out that she is the one who wanted to mutiny in the first place.
Once Young makes his way to Rush, Eli tells him about the tracking implant, which Young orders removed. Dr. Brightman is called in from Earth to help with the surgery while Eli monitors the shields, convincing Young that Rush had the right idea and attacking would only be a self-defeating effort. (SGU: "Divided")
The tracking implant is removed successfully and Destiny escapes to FTL relatively undamaged. Colonel Everett Young sends the civilians back to their quarters, confident that the mutiny is over, though also aware that this is not the end of the conflict between the two groups. (SGU: "Divided")