In CT, the player character’s ultimate goal is to defeat a near omnipotent alien parasite, Lavos. Lavos is a Lovecraftian-style Eldritch horror. Like Lovecraft’s own Cthulhu mythos stories, CT’s narrative is reactionary: it is about combating the inherently dangerous Other whose own reproductive strategy, while not necessarily intentionally malicious, is wildly orthogonal to our own goals and deleterious to our own survival. The Other and us have goals that are incommensurable, irreconcilable, and irreducible to such an extent that is an existential threat that is fundamentally incompatible with our being in the world. Our only option, however many pathways there are to the eventual true end and final conclusion—however many timelines and possible worlds—is to bring about the destruction of the Other. This is a deeply reactionary narrative.
In FFVI, the operatic story with a diverse ensemble cast culminates in the conflict between a megalomaniacal white male psychopath corrupted by powerlust as he is overcome by an empowered woman, who, in her Esper form, is almost a Mary Sue character. FFVI is thus a progressive story about the power of diversity and a female hero to overcome the existing imperial power structure and status quo. FFVI essentially embraces the World After the Fall, as this dystopian world of the archetypal anti-progressive villain, Kefka, who presides with godlike power over a wasteland of his own making (a totalizing system to which he would eternally enslave all living things)—which is itself a second order empire—is the one in which imperial power can finally be overcome. It is, in this way, implicitly anti-conservative in addition to being progressive.
Both games are art. Both games could be literature. Both games are genre-exemplifying. But their meanings are metapolitically incompatible. Chrono Triggers is less of a fantasy game in that it is realistic in its outlook: our natural world does undeniably contain destructive parasitism and combating it, through identification and elimination, is an organismal survival imperative. CT’s reference is firmly grounded in a rationally indubitable reality and it is thoroughly coherent, plot complications with time travel aside. It is for this reason that I believe the metapolitical realism of Chrono Trigger is superior to the dark high fantasy of the industrial opera, FFVI.