Comet Jo has spent his entire life tending the underground field of plyasil, a fictional crop of minor industrial use. The culture of his home is simplex, and space travel is not a part of it. He and his devil-kitten, D'ik, come upon a crashed spaceship while out walking one night. One of the ship's passengers, Norn, before dying, pleads with Jo to carry a message to Empire Star. Jo's growth into multiplexity and his journey to complete his mission—helping to emancipate the enslaved Lll—comprise the central storyline of Empire Star.
Although Jewel has a multiplex consciousness, in his crystallized state he cannot communicate with others unless he is directly addressed. He does, however, serve as Empire Star's narrator, at times addressing the reader directly. As the story progresses, it becomes clear that he—along with San Severina and Lump—are coordinating efforts to guide Comet Jo in the completion of his mission. All are part of an elaborate plan to emancipate the empire's enslaved Lll.
San Severina owns seven enslaved Lll, whom she has purchased to assist her in her task. She also plays a vital role in helping Comet Jo deliver his message to Empire Star. A princess of the empire, she watches over Jo during the first part of his journey, teaching him to speak properly. Jo encounters a 16-year-old version of San Severina as he nears the end of his mission. In Empire Star's final chapter, narrator Lump tells the reader that the elderly Charona, a childhood friend of Comet Jo's, is also San Severina at a different point in her life.
Lump was built to house the mind of Muels Aranlyde, a great Lll writer. He meets Comet Jo on Earth after San Severina has left Jo and accompanies him throughout most of his journey to Empire Star. Like San Severina and Jewel, Lump is part of a coordinated effort to help Comet Jo deliver his message, which will result in the emancipation of the empire's enslaved Lll.