The plot opens some time after the Moon Wars, where things for the original cast have taken a turn for the worse. the main character and pilot of Getter-1, Ryouma Nagare, has been framed for the murder of the Getter Machine builder Dr. Saotome after the death of Saotome's daughter, Michiru. However, he is released from jail and is reunited on Earth—unhappily—with his old allies, Hayato Jin (who set up then testified against Ryouma) and Musashi Tomoe, to fight none other than Dr. Saotome himself, who has seemingly risen from the grave to threaten humanity with his ultimate creation—and most dangerous weapon—Shin Getter Dragon, a massive weapon powered by the same cosmic Getter Rays which gave life to their old weapons. However, their efforts to stop Dr. Saotome, not to mention an overzealous Japanese Defense Force, are in vain, as nuclear weapons are used on Shin Dragon.

The resulting explosion and shock wave of Getter Rays wipes out 99% of the human population worldwide. Thirteen years after this catastrophe, as humanity clings desperately to life, the re-emerged extraterrestrial Invaders threaten Earth once more. The only safeguard against this alien threat is a giant robot that emerges from the wreckage of the nuclear blast—Shin Getter Robo—piloted by an artificially created human named Gou. With the help of Hayato's Super Robot Army and Gou's co-pilots Kei and Gai, Shin Getter fights to keep humanity's dreams alive.

Later, Ryouma returns piloting the Black Getter Robo to aid the new Getter team against Dr. Saotome who returns with Stinger and Corwen when Shin Getter Dragon re-activates and continues its evolution. It was also revealed that Kei was Dr. Saotome's younger daughter and Michiru's younger sister, who was adopted by Benkei. Soon the Invaders put their true plan into action by transforming Jupiter into a Getter Ray Sun and Ganymede one of its moons would soon go on a collision course with Earth, prompting both the old and new Getter teams to spring into action to save the planet.