ladygrimblossom:

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You know, this is a really important sequence in the episode.

Not

because John is about shut down EOS. Because that’s what the episode has
been building up to. Its important, and particularly with EOS’ words.
Even though EOS is a child, she’s very much a victim of her own
circumstances. She’s alone and afraid, and even without any kind of
visual emotional cues, you can tell the isolation is terrifying, and the
prospect that she’s about to die is makes her incredibly sad and
fearful.

But its also a crucial part of John’s character as well.
He’s spent the first half of the  episode trying to convince EOS that
he’s not a threat to her. And the Second half begging her to listen and
saying he doesn’t want to hurt her at all. He wants to help her,
understand her and look out for her. Like another sibling, or more
appropriately a parent to a child.

Even at the very end, this
his hand over the button for emergency shutdown, he’s borderline begging
her to stop, pleading with her that he doesn’t want to do it. Hell,
even before, when he was in Thunderbird 03 being ordered to destroy EOS
if that’s what it took, John really didn’t want to do it. He
continues to try and reason with her, even when EOS turned the gravity
ring on max spin and Alan stops it, John already treats her as Thunderbird 5, lightly warning her not to damage herself trying to take
him out.

Here in this scene, John’s still very hesitant with
his hand over the shutdown. At this point, if you read between the
lines:

He’s begging EOS not to make him a murderer.

The following scene where he takes his helmet off, to me, that says ‘I would rather die than become a murderer’. It just says so much about his character that he would rather die than compromise his ideals and the ideals of his family.