The criminal organization BioNet steals one of the Q-Parts being researched at CERN. This episode serves primarily to introduce the changes to the main cast since the end of the series. Guy debuts in his new Super Mechanoid GaoFighGar, a combination of upgraded GaoMachines and the reconfiguring jet PhantomGao that was built to replace Galeon after the latter's departure from Earth at the end of the series.

Mamoru takes the rest of the Q-Parts, either by guile or by force, and assembles them into their full form, a matter replication device known as the Pas-Q Machine. In the process, Papillon is killed, and Guy takes after Mamoru. The encounter ends in a battle between GaoFighGar and a copy of GaoGaiGar using Mamoru and a bleached version of Galeon as the core component. The battle ends in Guy's victory (at the cost of the helper robo Goldymarg, causing Guy to use Hell and Heaven as his finishing move once again), and both Mamoru and Galeon are revealed to be replicants that dissolve into sand. The machine is promptly taken by a mysterious man with butterfly wings, and GGG prepares to take after him into space.

In order to get around the United Nations' refusal to allow them to leave Earth, Gutsy Galaxy Guard stages an elaborate ploy together with their related organizations and the Secretary General of the UN, Rose Approval. The result is that three of GGG's Division ships and their crew (that is, the entirety of the main cast) are exiled from Earth, and are free to follow Ikumi Kaidou's directions to the Trinary Solar System. Their enemy is revealed to be the 11 Planetary Masters of Sol, programs designed to regenerate the Trinary Solar System after the Z-Master was eradicated.

GGG arrives in the Trinary Solar System to find a replica of Earth - like all the previous replicants, this is an off-color version. Its only inhabitant is a replica of Papillon Noir, who reveals that this replica of Earth was created moments prior to her original's death by a misfire of the Pas-Q Machine. As it is only part of the complete regeneration machine, the Pas-Q Machine can only produce imperfect duplicates. Papillon was the only human duplicate that was stable enough to survive for more than a few seconds. The Galeon and Mamoru previously met were also Pas-Q Machine duplicates.

Guy finishes his fight with Palparepa, followed by Mikoto's awakening from her slumber. Papillon reveals that Mikoto is an invincible lifeform like the new machine species Zonuda, and thus was able to recover from the nerve-relaxing Paras Particles Palparepa had spread across the Repli-Earth. Papillon begins work on an antidote, while Mikoto goes to find the imprisoned Soldato J, now mankind's last hope. In the process, she meets the real Mamoru, who had been in the Trinary Solar System for a year and a half. Upon meeting and freeing J (with the help of Renais), Mikoto is attacked by the Sol Masters Pillnus and Pia Decem, respectively Renais and J's counterparts. The heroes escape on the reborn J-Ark, which is dragged up into the upper atmosphere and forced to do battle with replicants of the entire Mobile Unit and a replica of GaoFighGar piloted by none other than Guy, now under Palparepa's control.

The Soul Masters attack J-Ark directly, and in the process Guy, Mamoru and Mikoto escape to the G-Crystal located on the replica of the moon. The G-Crystal is the only thing left from the original Tri-Solar System, and it is here that Mamoru has been hiding out all this time, working to restore Galeon to its original form and programming. Guy performs Final Fusion for the last time to form the God of Destruction, Genesic GaoGaiGar.

Genesic GaoGaiGar demonstrates its sheer destructive power against the 11 Planetary Masters of Sol. The Gutsy Galaxy Guard arrives partway into the battle, cured of the influence of Paras Particles. The members of the Mobile Unit (as well as J-Ark) end up faced off against their counterparts, with Soldato J's power being restored and enhanced by proximity to Renais Kerdif-Shishioh's G-Stone. The battles end up spread across the entire Repli-Earth, and Genesic GaoGaiGar's fight with Palparepa is shown to be very one-sided until Palparepa powers up by injecting himself with his own Doping Cylinders. The episode ends with Palparepa using his improved God and Devil as Guy unveils the true form of Hell and Heaven.

GGG fares well initially against each of the 11 Planetary Masters of Sol, but the Masters are capable of regenerating infinitely, and ultimately manage to overpower the heroes. Each member of the Mobile Unit uses their desperation attack, most of which were formerly only listed in tech specs, and emerges victorious. Guy manages to defeat the powered-up Palparepa even after he undergoes yet another transformation, and reveals that the G-Stones convert courage into life force. Against this power, the Loud G-Stones that power the Masters lose their strength. The Masters' Regeneration Machine, controlled by Pisa Sol, proceeds to duplicate all the destroyed Masters a hundred times over. This temporarily drains its stored power, giving GGG the opportunity they need to use their ultimate weapon, the Goldion Crusher, to destroy it and thus end the menace of the Masters. Unfortunately, GGG is faced with the discovery that this Repli-jin universe is collapsing, and the only chance for escape lies with J-Ark's two remaining ES Missiles. In the end, Mamoru and Kaidou are sent in out of the system, bidding tearful farewells to their comrades. Upon their return to Earth, Mamoru, Kaidou and Hana create a memorial to honor GGG's sacrifice.