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...

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.