Weeks after the dust settles from Sosai X's destruction, a tiny fragment of the alien revives and begins to rebuild itself into Sosai Zed. Using the remains of an old shipyard, Zed builds a vast mechanical pyramid fortress and levitates it over the ocean. Meanwhile, the rest of the world quits rebuilding from the wreckage of the thwarted Solar Shift Plan and go back to what they do best: waging war. We meet Count Egobossler, successful ruler of a growing number of territories, and an aspiring megalomaniac. Egobossler meets Sosai Zed, who decides to use Egobossler's brilliant military tactics to his own advantage, and the two strike a deal. In the wake of Chief Anderson's death in Gatchaman II, Nambu is promoted to Chief Administrator of the ISO. The Kagaku Ninjatai cope with the unusual peace. Feeling useless during peacetime, Joe wallows in boredom and self pity while Nambu tries to find a way to recharge him after his near-destruction in G-II.

Egobossler's first attack, backed up by one of Zed's giant mechs, completely startles out heroes. Ken, Jun, Jinpei and Ryu rush to the scene of the battle (leaving Joe behind to quietly expire). The mech is too powerful, and the New Godphoenix is completely trashed in the first skirmish with Egobossler. Fortunately, Chief Engineer Saburo Kamo is waiting in the wings with brand new mechs. With only one problem: the new vehicles need five operators to combine. It's up to Joe, who upon hearing the phrase, "Gallactor has returned," will crawl on his final strength to rejoin the team. TheGatchaspartan saves the day.

Ken asks the same question viewers have probably been asking since the beginning: "Enough battling the little guys--why can't we meet Egobossler head on?" The Team does, but fails miserably. This episode ends in a very disturbing role reversal scene with Ken--now beyond reason--raging at a laughing Egobossler, and Joe finally having to bring all his strength into play to drag Ken back into the Gatchaspartan.

The Kagaku Ninjatai continue their tries at direct confrontation by stealing aboard Zed's tower and facing him directly. This doesn't work either (can we say "outnumbered"?), though they do get in a few good punches.

Mercenary scientist Professor Gordon develops an indestructible material called Neophryte and decides to sell it to the highest bidder. So he summons agents from both Gallactor (Egobossler's first officer, Kempler) and the ISO (the Gatchaman, naturally) to meet alone on a spot he specifies. Of course Kempler doesn't come alone, but much to both his and Ken's surprise, neither does Ken. While the Gallactors and the rest of the Kagaku Ninjatai take part in a snarling standoff outside, Gordon, Kempler and Ken negotiate. Kempler offers money, while Ken refuses to haggle, stating honor and decency as his reasons (and knowing as Gordon does that once he withdraws his protection, Gallactor will simply take what they want by force). Worried about his father, Gordon's son finally ends the standoff and uncovers the compound for both sides to fight over. Joe uses a bazooka loaded with Neophryte to blow a hole in the monstermech that appears at the end.

One of Egobossler's old friends and colleagues Oncain, is also the last man on Earth who knows Count Egobossler's deep, dark secrets. The Kagaku Ninjatai get to Oncain first and try to convince him to stay away from Egobossler, but the man will have nothing of it. He invites the Team to go fox-hunting and with his two children, Michael and Mary, and as they're distracted, arranges to meet with Egobossler. The inevitable showdown with Egobossler and his special Skyrider command is spectacular, but even Ken and Joe at their best can't prevent Ego from gunning down his man. Joe comes round the corner just in time as Ego shoots Oncain right before Michael and Mary's eyes (triggering a flashback where you almost see the faces of Joe's parents). In the final scene, Joe kneels down and has a little heart-to-heart talk with Michael. You don't hear what he says, only Michael's reactions.

The Team searches for Zed in his tower, and are thrown around like playthings. When they finally meet up, they discover what happened to Egobossler: his corpse is pinned against a wall in Zed's main chamber, run through by his own sword. At this point, Joe picks up on Zed's vital signs (as Rafael had designed him to) and tracks the alien to his last refuge, where the Kagaku Ninjatai battle to destroy him... and fall. Chief Nambu's mysterious pendant (an unanalyzed device he'd instructed Kamo to give to the Team before the last battle) comes into play then, activating the Gatchaspartan and swallowing the fallen ninjas with light... The final scene is of an enormous firebird breaking free of Zed's exploding tower and flying around the Earth, leaving us to analyze the wide open ending. (Chances are high, though, that they aren't dead--they're still under contract, after all.