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The Destiny master code is a code based on an advanced Ancient DNA sequence. This code is required to access most of the main systems aboard Destiny like navigation and advanced power management but not for basic weapon and shield control. Dr. Nicholas Rush discovered the master code and kept it a secret as well as his discovery of the bridge for some time. Eventually, the rest of the crew were able to find the bridge and Rush had to come clean about his discovery of the master code. With the code, the ship can be piloted from the control interface room as shown when Rush and Eli piloted it through a blue giant when the bridge was locked down due to lack of power. (SGU: "Human", "Aftermath", "The Greater Good", "Blockade")