Destiny is set seven hundred years into the future in a post-apocalyptic setting following a prosperous period of exploration, peace and technological advancement known as the Golden Age. In a universe where humans have spread out and colonized planets in the Solar System, an event known as "the Collapse" saw the mysterious dissolution of these colonies, the end of the Golden Age, and mankind teetering on the brink of extinction. The only known survivors of the Collapse are those living on Earth, who were saved by "the Traveler", a white, spherical celestial body whose appearance centuries before had enabled humans to reach the stars. The Traveler now hovers above the last remaining human city, and its presence allows the "Guardians of the City"—the last defenders of the human race—the ability to wield an unknown power.
Upon mankind's first attempt to repopulate and reconstruct after the Collapse, it is discovered that hostile alien races have occupied mankind's former colonies and civilizations and are now encroaching upon the City. The player takes on the role of a Guardian of the City, and is tasked with investigating and destroying these threats before humanity is completely wiped out.