Brainiac and his robotic minions are invading Earth, and a final war between superheroes and villains have left humanity defenseless. In desperation, Lex Luthor travels back in time to warn his foes, and at the same time, litter the planet with the seeds to create new heroes. As one of these newly-transformed superhumans, players will choose to save the planet from Brainiac for the good of humanity, or to their own nefarious ends.

As an action MMO in the DC Universe, DC Universe Online will pit players with or against each other under the watchful eyes of major comic characters. Upon starting a character, players can choose to be a hero or a villain, with the tone and specifics of their missions changing accordingly. Next, they choose a mentor - Superman, Batman, or Wonder Woman for heroes, and Lex Luthor, The Joker, or Circe for villains. Though players will take missions from many different DC characters, this mentor will guide their overall progress to the level cap.