N finds out purely by chance. They meet in Lostlorn Forest, because Galvantula spots the other trainer and decides to be helpful, stealing his cap so that he'll have to chase after them and run into Touya. Touya doesn't know what to make of hir Pokemon trying to orchestrate meetings between hir and the apparent King of Team Plasma, but sie doesn't comment, just passes N his cap when he finds hir and hopes that he won't challenge hir to a battle this time.
He doesn't, although he does spot Touya's nails as sie hands over the cap, colored blue because sie's actually bothered to paint them for once, no matter that the nails themselves are bitten and ragged. N cocks his head to the side in a birdlike motion, catching hir hand before sie can pull away.
"I didn't think boys were supposed to wear nail polish," he comments, all innocence.
Touya flinches, despite hirself, and N blinks. He looks hurt himself, and Touya finds hirself rushing to reassure him, no matter that it's not like sie's actually done anything wrong, "I'm... androgyne. It's... it's not your fault for assuming, though..."
To hir surprise, N immediately perks up, informing hir, "Oh! I've read about that! So, you don't see yourself as a boy or a girl?"
He seems content to babble on about what he's read on the subject, once Touya has confirmed it for him, and sie's just as happy to let him talk. It means that sie doesn't need to say anything hirself, doesn't need to try to explain it to somebody who doesn't want to understand how sie feels or why. As he talks, they walk slowly back to Nimbasa, and when they arrive at the Pokemon Center N buys a two-bed room for them to share and Touya can't even bring hirself to complain or refuse.
He's gone in the morning when Touya wakes up, his bed as pristinely made as if he'd never slept, but when sie arrives in Driftveil, there's an anonymous package left for hir in the Center that holds a gender studies textbook and a bottle of nail polish the exact same shade of green as N's hair.
It's an odd gift, yes, but it's so very much N, and Touya finds hirself blushing so much that the woman at the counter asks if sie's okay.
"Yes," Touya tells her, and sie means it. N knows, and he's okay with it and giving hir gifts to show that he understands, truly, and if Touya's throat is tight and hir heart is racing at that, it's only because sie doesn't think anybody has ever understood it so truly as N, no matter that he's not non-binary himself and he's probably never gone through the confusion that Touya did when sie first started to realise. He's N, and so he understands, maybe as much as he understands Pokemon.
Maybe as much as Galvantula understands humans, sie thinks, because if the spider had never stolen N's cap then none of this would have happened.