The Comet Empire is the name of the second series of Starblazers. In Japan it is named only "Yamato 2". It was based on the movie Arrivederci Yamato and lengthened into a full season. The year is 2201, and the Earth has been at peace after war with the Gamilons. Now a new threat called the Comet Empire streaks towards Earth, devouring planets in its wake. Zordar, Prince of the Comet Empire, intends to conquer Earth and make its inhabitants slaves.

While patrolling around Jupiter, the Yamato encounters strange alien ships. After returning fire, the ships scatter and the Yamato retreats. On Earth, the ship is repaired and Derek Wildstar tries to convince the Earth Defense Council there is danger from space. The Yamato takes off secretly against orders when they hear an urgent radio message from outer space. The woman identifies herself as Trelaina of Telezart. She urges the Star Force to find Telezart so that she may help the Earth.

Much to the Star Force's dismay, Desslok has survived from the last battle and is serving the Comet Empire. He encounters the Star Force many times, but naturally never catches them. Invidia tries to trick Desslok and her father Zordar and gain power of the Comet Empire, but she is found out. However, it does provide some good scenes between Desslok and Invidia. Upon reaching Telezart,Mark Venture falls in love with Trelaina. He asks her to accompany him, but she refuses. She slows down the Comet Empire by turning Telezart into energy and firing it at them. She does survive and continues to contact the Star Force.

During one of the last battles, the entire Earth Defense Fleet is wiped out, and the Yamato badly damaged. They ram the Yamato into the Desslok's flagship and evacuate. Derek Wildstar sneaks into the ship and finds Desslok there. Desslok refuses to shoot Wildstar after he sees Nova's love for him. He is a changed man (somewhat) and agrees to stop hunting the Star Force. On the way to Earth, the Yamato tries to destroy the Comet Empire by shooting it from beneath. However it is Trelaina who destroys them for good, turning her body into energy.

The planet Comet Empire is a large city perched atop a moon-like planet. It is also called "Gatlantis". The diameter of the city is 15 km, and the structure as a whole is 10 km tall. It is protected by a shield of white plasma, which also serves as a matter of absorbing space fuel by crushing planets. It also has a revolving gunnery around its middle, and several guns located on the bottom of the city to protect the hangar. When the Comet Empire was destroyed, Zordar, Invidia and General Guile escaped on a huge dreadnaught located under the city.