Having murdered the attacking musuca, a whale-like biological amalgam developed by Zorndyke featured in the closing scene of "Blues," the Blue forces face the Phantom Ship at the opening of "Pilots." Zorndyke's flagship proves too much for the whole fleet, driving Blue 6 out of the battle that eventually destroys Tokyo. It's home decimated; the Blue 6 crew regroups with the Pacific Fleet at an elaborate underwater stronghold where world leaders strategize a way to strike at Zorndyke directly. But a briefing of the plan is interrupted by a message from Zorndyke, a haggard, woeful man, admonishing this military clan that attempts to stop the course of events he has set in motion will come to naught. Zorndyke's complacency only inspires a more rooted determinism within Blue Fleet. However, Hayami reads deeper into Zorndyke's reasoning. His utter detestation for Blue Fleet's bellicose plans, undermined only by his involvement in those plans, seeps into the narrative and, again, hints at Hayami's enlightenment.

Amidst the flurry of sub-aquatic battles in "Pilots," scriptwriter Hiroshi Yamaguchi hews closely to the headier themes. In fact, he even makes the violence itself a commentary on the chaotic impulses of human nature, essentially turning the good guy/bad guy axis on its ear. Director Mahiro Maeda continues to shape the anime along these lines, blurring the notions of good and evil in an attempt to expose both as the result of misguided righteousness: The "good" Blue Fleet champions the survival of a mankind that has systematically dismantled the world's eco-systems; the "bad" Professor Zorndyke feels that humanity can no longer learn the lesson of environmental decay and, therefore, shouldn't survive. Only Hayami recognizes the hypocrisy evident in both mentalities.

"Pilots" fleshes out the global scene. The Atlantic and Pacific Fleets, assembled from the tattered remains of the world's national navies, plan to strike at Zorndyke's Antarctic compound. The Admiral of the Atlantic Fleet has a personal grudge against Zorndyke, his attacks having caused the death of her family. Her fleet plans to make the main strike. (And kudos to the progressive vision of the "Blue Sub" design team for making the Admiral a black woman, an ethno-gender combination that seldom makes it into anime.) Head of the Pacific Fleet, Dr. Marunami, a diminutive, bespectacled intellectual with cybernetic implants in his skull (a telling symbol of his sickly body and mankind's reliance on technology) masterminds the attack.

The madman's threat is made more concrete with the revelation that Zorndyke has developed a machine in the Antarctic that slowly shifts the poles causing the dissipation of high-energy particles in the Van Allen Radiation Belts. But Maeda doesn't score the discovery of this apocalyptic plan with a dark musical motif. Nor does he punctuate it with a villainous visage cackling loudly with ill-founded confidence. Zorndyke is hardly an exhibitionist. His earnest disappointment in his own species pours through his words in a message to Blue Fleet. Spoken with a soft tone reminiscent of a father mollifying the fears and pain of a terminally leukemic child, the speech introduces an antagonist who understands the gravity of his actions but proceeds with his ostensibly evil plan anyway from sheer lack of hope. However, Zorndyke's military coordinator, Verg, is just a brutish, abusive, salacious wad of evil. A shark-like humanoid with a shrill voice, Verg represents the typical face of the enemy in anime. Of course, Zorndyke sends him to defeat the Blue Fleet because of his savagery, fighting fire with fire so to speak.

As Zorndyke's forces attack the Pacific Fleet headquarters, Marunami orders an evacuation but stays behind to run the control room and, eventually, perish in it. As the ceiling caves in around him, Marunami speaks directly and familiarly with Professor Zorndyke. The madman's betrayal is not only against humankind, but also against individual friends.

Hayami, who in the first episode states 'it is already too late for our world,' unwittingly shares Zorndyke's sentiments. His loyalty, though, belongs to the Blue Submarine No. 6 crew, however cynical or uncooperative he may be with it. Therefore, rather than dismiss mankind he is poised to bridge the gap between Zorndyke's concerns and Blue Fleet's perception of them. The amphibious woman from the first episode, a sea monster to the rest of the human characters, closes this chapter with the same sense of compassion and reason taking root in Hayami. He is not alone, nor is the enemy who they seem.

Though voiced numerous times both in anime and the wider field of entertainment, never has the cry indicting mankind for global warming been sounded so poignantly. These weighty dynamics may be obscured by the visual splendor of "Blue Submarine No. 6," but they drive this story toward a profound ending.