According to my observations of Mikoto, she’s a neutral character. In the story of FFIX, she is portrayed as a character of sympathy. Initially, she is working for Garland’s orders to lead Zidane to him. Then as Terra is falling apart, she is unsure of what to do. Zidane convinces her to join him in a newer better life without Garland. I’m sure she realized beforehand that her oldest brother had kicked Garland over the precipice into oblivion. So she lets him convince her to leave her homeland and she joins the other Genomes Zidane’s party managed to save onto the Hildegarde III, and ultimately she and her siblings end up in the Black Mage Village. Amarant comments on their “childish” behavior, so it appears that the Genomes are excited to interact with a new world. Mikoto alone is thoughtful and conscious of what has been going on.
But I was under the impression that they were soulless, and void of emotions as Zidane had noted earlier?
One needs to define what exactly a soul is. A soul is the spirit force that lives on beyond the physical body. The soul is capable of feeling, and helps to guide the physical body in moral/ethical thoughts and actions. A soul makes a person significant in the grand scheme of life: without a soul, a person would be void of purpose, no different than an android functioning without meaning in their actions. Androids function, fulfill their master’s commands, then follow orders for whatever they’re programmed for next. A soul gives meaning to living.
A soul is typically in accompaniment with religion. Currently, the majority of civilization in FFIX doesn’t appear to acknowledge any religion. Those in Esto Gaza worshipped the Shimmering Island. The Summoners were truly the main religion of Gaia before Garland destroyed Madain Sari in an effort to keep the eidolons to himself. In destroying Madain Sari and the Summoners, religion took a dive into indifference and technology and information took precedence.
In creating soulless Genomes, it makes me wonder if Garland had another scheme for creating them that way. Did Garland function under the Terran’s rules and regulations as programmed by his Terran designers? We already know that Genomes are what they are, and they always will be unless their physical body is compromised (they are immortal, though how that is supposed to work, I don’t know). Genomes are essentially androids during Garland’s reign, they follow him blindly, and even Mikoto just assumed they had no choices of their own.
So when Zidane enlightens her of a new life without oppression, she accepts. But how whole-heartedly did she accept? She acknowledges Kuja’s influence and the role he played in their “father’s” grand scheme at the end. She acknowledges Kuja’s desire to defy his fate. And she wishes to keep his memory alive, according to his eulogy. Does she intend on teaching the Genomes and others of Kuja’s manner of living? How can she teach a soulless Genome the meaning of living? Or does she intend on something more?