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.