The criminal organization BioNet stole one of the Q-Parts being researched at CERN, which has high regenerative properties. The Gusty Galaxy Guard appointed Guy Shishioh to work with his half cousin Renais-Kardif Shishioh and biologist Papillon Noir in Paris, France. Debuting with the new Super Mechanoid, GaoFighGar, Guy alongside GGG managed to defeat one of BioNet's agents and retrieve the Q-Parts. However amidst of their victory, a pale colored Mamoru Amami appeared after a year of his departure...

Upon the appearance of Mamoru, he then stole one of the Q-Parts as he collects the rest of them, 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 off after Mamoru. The encounter ends in a battle between GaoFighGar and a copy of GaoGaiGar using Mamoru and a copy of Galeon as the core component. The battle ends in Guy's victory, 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

Due to the unfortunate events regarding the Q-Parts, GGG attempts to get around the UN's refusal to allow them to leave Earth. The group staged 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 Tri-Solar System. Their enemy is revealed to be the 11 Sol Masters, sentient programs designed to regenerate the Tri-Solar System after the Z-Master was eradicated.

GGG finally crossed the Galeoria comet and arrived in an alternate universe controlled by 11 Sol Masters. GGG arrive 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, who reveals that this replica of Earth was created moments prior to her original's death by a misfire of the Pas-Q Machine, which produces 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. GGG scours the Earth for Mamoru and the Sol Masters, but fails to find so much as a hint of them. Over time, the majority of GGG becomes lethargic, and most eventually slip into sleep. The Mobile Unit is shut down by them prior to this, leaving only Guy, Papillon and Renais active. Guy hunts for the source of all this, and is accosted by the Sol Masters. He faces off against Palparepa, the man who stole the Pas-Q Machine, but falls against Palparepa's God and Devil attack when he sees that one of the Sol Masters is Cain, leader of the Green Planet.

GaoFighGar is destroyed by Palparepa, and Mikoto awakens from her slumber. Papillon reveals that Mikoto is an invincible life-form like the new machine species Zonder, and thus was able to recover from the nerve-relaxing Paras Particles Palparepa had spread across the replicant 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 Tri-Solar System for a year and a half. Upon meeting and freeing J (with the help of Renais), Mikoto is attacked by two more Sol Masters - the bee-like Pillnus and the reaper-like 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 fight between King J-Der and GaoFighGar concludes and results in Guy's purification. J's J-Quath is shattered in the fight after the Repli-Mobile Unit rebel and sacrifice themselves to take some of the blow from the Repli-Goldion Hammer, destroying the Repli-Goldymarg soon afterwards. 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, while J finds his J-Jewel shut down. 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. The Sol Masters attempt to destroy the Crystal, and their duplicate of Cain attempts to conduct Fusion with the new Genesic Galeon. It refuses, and instead reveals that Guy is within, alive and well. Guy conducts Fusion with Galeon, and Mikoto breaks a crystal plate to release the Genesic Machines, the original GaoMachines. Guy performs Final Fusion for the last time to form the God of Destruction, Genesic GaoGaiGar. Mikoto, however, is critically wounded in the aftermath. She is left nearly dead - however, if what Papillon said is true, Mikoto cannot die.

Genesic GaoGaiGar demonstrates its sheer destructive power against the Sol Masters until Palus Abel decided to unveil her trump card: fusing Pisa Sol with the Replica Sun and increasing the PasQ Machine's regenerative powers. GGG arrives partway into the battle, now awakened by Papillon's antidote. The members of the Mobile Unit (as well as J-Ark) end up faced off against their counterparts, with J's power being restored and enhanced by proximity to Renais's G-Stone. The battles end up spread across the entire 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. Palparepa uses his improved God and Devil as Guy unveils the true form of Hell and Heaven.

In the final battle against the 11 Sol Masters, GGG fares well initially against each of them. However, the Soul 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 Sol Masters lose their strength; furthermore, the G-Stone's power can grow indefinitely, exceeding the Loud G-Stone's limit. As the Sol Masters fall, their Regeneration Machine - Pisa Sol - proceeds to revive and duplicate them a hundred times over. This drains its 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 Sol Masters. Unfortunately, GGG is faced with the discovery that this Repli-jin universe is collapsing, and there is only a 1-meter gateway that will be open for 2 seconds for anyone to escape. In the end, Mamoru and Kaidou are sent in torpedoes out of the universe, bidding tearful farewells to their comrades. Upon their return to earth, Mamoru, Kaidou and Hana create a memorial to honor GGG's sacrifice.