About a year after the battle with the Hyakki Empire, the Getter team returns to Saotome Labs while dealing with the Dinosaur Empire. Later, a huge meteor comes crashing from the sky and the Getter Robo and Getter Robo G are powerless to stop it. The meteor, however, is revealed to, in fact, be their thought to be dead enemy Emperor Burai. With Burai putting up a fight, Dr. Saotome decides to unleash the newest Getter robot, Shin Getter Robo. The tables have turned but Burai tells the Getter team that he was revived by someone who bore a grudge against the Getter.
This same group continued to appear in an attempt to destroy the Getter Ray research having come from a future that was ravaged by the appearance of the Getter Emperor. Benkei attempted to fight off this new enemy in the Getter Robo G but was driven underground and the fission of Getter Energy had killed him while changing the Getter G in a slow but gradual process into something else entirely. Dr. Saotome begins to show obsessive behavior with the Getter Rays and even sees the spirits of fallen enemies and allies who have agreed to use the Getter to destroy the new threat.
During an experiment to test Shin Getter, Ryoma witnesses an apocalyptic future where humanity has taken to space in Getter machines headed by Getter Emperor. Here, the Emperor is shown as being on a scale where planets are threatened by its mere existence. Meanwhile, Hayato starts to take an interest in Getter Rays especially where the human element is involved while developing a Getter machine that runs on plasma rather than Getter Energy. Ryoma begins to have doubts about the Getter Rays but the prototype Getters suddenly begin to act on their own and Getter Dragon begins to sink deeper underground in its cocoon of Getter Energy. As the enemy army continues to attack, Shin Getter is used to push them back. Ryoma begins to question about Shin Getter and the future he previously saw.
Before Ryoma could fully confront Dr. Saotome, the mysterious enemy from before attacks again going after the evolving Getter Dragon. Ryoma and Hayato goes after them and manage to push them back with the power of the evolved Dragon. Shin Getter Robo and the enemy vessel are soon sent forward through time, where Getter Emperor destroys the comparatively miniscule vessel. Ryoma and Hayato ponder the meaning of this distant future, but are returned back to their own time. But even though the battle was won, the Saotome Institute is overwhelmed by Getter Ray radiation from the Getter Dragon's cocoon with everyone being wiped out. Only Ryoma and Hayato had survived to witness the deaths of all their allies.