As with its predecessors, The Interpretaris and Vega 4, Phoenix Five took its name from the spaceship that was the show's focus: the flagship of Earth Space Control, with a two-man, one-woman team, assisted by their computeroid, Karl. The show had two primary villains. For the first thirteen episodes, the villain was Zodian (the evil scientist of Vega 4, now re-cast and with a newly blue skintone), who sought galactic domination from his base on Zebula 9, with the support of his twin computers, Alpha and Zeta. When Zodian was captured, he was replaced as villain by Platonus, assisted by a computer called Tommy.
Rather than following a single story arc as its predecessors had, Phoenix Five was a series of self-contained stories, allowing the script writers to move freely around the galaxies, and explore whichever crisis the crew happened to come across.