After Destiny left the previous galaxy and entered the void on its way to the next one, one of the ship's FTL drives exploded, setting the ship adrift in the void. Investigation revealed that the drive overloaded, and though in the long run it would prove to be beneficial, the necessary repairs to bypass the damage and reengage the drive would take weeks.
Destiny's problems also had the benefit of allowing Eli Wallace, Chloe Armstrong, and Lt. Matthew Scott to return from the planet they had been stranded on. When Colonel Everett Young arranged for a team to go back to the planet and gather supplies, they discovered two Nakai fighters guarding the gate. Later on, they realized that Destiny had been sabotaged by a Nakai who had taken control of Lt. Vanessa James using the Long-range communication device. James had earlier used the device and forgot to clear her imprint from the Long-range communication stone she used. Eventually, two Nakai motherships dropped out of Hyperspace and began their assault. (SGU: "Sabotage")
The Nakai motherships sent out waves of Nakai fighters to board Destiny while attempting to deplete the shields. Lt. Matthew Scott, Eli Wallace, Dr. Dale Volker, Dr. Adam Brody, and Dr. Amanda Perry manned Destiny's weapons systems and concentrated their fire on the fighters, though they were unable to stop them all. Meanwhile, Colonel Everett Young prepared to use the Destiny interface chair to bypass the damage remotely and take Destiny to FTL. However, Jeremy Franklin, having recovered enough motor function to just barely make his intentions known, volunteered himself instead. Franklin successfully bypassed the damage and took Destiny to FTL, destroying the fighters attempting to dock in the process. (SGU: "Sabotage")
With the damage bypassed, Dr. Nicholas Rush calculated that the ship will be able to make it into the next galaxy. Jeremy Franklin, after finishing his work, mysteriously disappeared. It's later revealed that his consciousness was downloaded into Destiny's mainframe. (SGU: "Sabotage", "Hope")