Y’all have @Wolven to blame for this thread.

First: Tom is relying on a Japanese understanding that humans who aren’t moved by the world (nasakenaishi) aren’t really human, so his words are affirmations of Fukai’s humanity and the nature of humanity, the kokoro. https://twitter.com/shaunduke/status/1262838895424598016
Which Tom is characterizing as different than the JAM kokoro. We can imply that Tom “becomes” human by being a JAM embodied as a human and thus developing his kokoro in transaction with other humans, rather than JAM.
Which is not, by the by, a Cartesian move: it’s an argument for the self as relational and embodied, as touched and touching others. It’s implied that the JAM don’t have this kind of self, which drives their attacks on Earth.
(Fun fact: Gundam 00: A Wakening of the Trailblazer has some of this with the ELS as a single organism that can communicate only through assimilation. The protagonist uses his Gundam to touch the kokoro of the ELS and achieve understanding.)
This gets me to Yukikaze (WARNING LT. FUKAI) and it’s relationship with Fukai himself. Now, the piece is right about trusting the machine, but misses the mark in describing Fukai’s relationship with Yukikaze. It’s transactional.
Fukai comes to learn the kokoro of Yukikaze through flying it, in the same way we come to know the kokoro of our cars through driving. The distinction is that Yukikaze comes to know Fukai’s kokoro as well and they form a deep affective bond.
(Side note, Wing Zero seems to have this relationship with Heero Yuy in Endless Waltz. My read of the post WuFei fight is that Zero convinces Heero to go help the other pilots when he’d given up.)
(We also see this with Chamber in Suisei no Gargantia, Fuego in Rideback, and shades of this with Alphonse in Patlabor. Chamber is the only AI of the bunch, but the rest share an affective connection with their partners.)
My read of Fukai’s catatonic state post ejection is a kind of grief at potentially losing his partner, an entity that understands Fukai’s kokoro in a way that others cannot. Also, who knows what the JAM did to him on Fairy.
Now, the interesting thing is that the JAM tried to dismantle Yukikaze to understand it, but they couldn’t. They knew it was AI and a machine, but they couldn’t fathom its kokoro which the series implies is the source of its ability to detect JAM.
There’s also some indication that the humans don’t understand Yukikaze’s kokoro either as iirc, they couldn’t duplicate it and it actively refused to engage with other pilots. My memory is fuzzy here.
In any case Fukai trusts Yuki and Yuki trusts Fukai but because they understand each other’s kokoro, their heart/minds such that they are interdependent in their activity. Symbiosis might capture this, but not accurately as it doesn’t explain some of Fukai’s mannerisms.
Again, iirc, Fukai experiences a longing for Yukikaze when he’s grounded and not on base, which can be dismissed as the longing for flight, but I read it as the absence of his connection with Yukikaze. He is fully himself when he’s with the machine that knows him.
We might think of this as the person who is “alive” with their partner, or “lights up” in their presence. Same with Fukai and Yukikaze, which is why the ending makes a lot of sense in this context. Fukai wouldn’t let Yukikaze go alone because of their connection.
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