I know some people are not a fan of Spider being able to breath Pandora's air because it takes away Spider interesting backstory of someone living on a planet that's completely inhospitable to him and the challenges he overcomes but..
BUT I really love the idea of Spider one day, maybe he accidently knocks his mask off his face and at first he panics but then nothing happens. He can breath the air! He doesn't need the mask to breath when he could be the air. And the first thing he wants to do is leave.
Yes, leave. It's sad, but he's had enough.
Enough of the hatred he gets from Neytiri, the feign ignorance Jake displays when he ignores how his mate treats him. Enough of the mistrust of the Omatikaya. Enough of being ignored or being seen as a burden by the scientists.
And he just decides to run away, just leave both the Omatikaya and Hell's Gate behind. He's no longer tethered to Hell's Gatw because he doesn't need assistance to breath.
Spider wants to explore all of Pandora. He wants to see every inch of Eywa's beautiful creation. Spider has never really belonged anywhere, why should he stay in one space?
He'll miss Kiri, Lo'ak, Tuk, Mo'at, and even Neteyam. They were the only ones who were good to him even if Neteyam had started to pull away. He will miss them all but as their mother has constantly tells Spider, he doesn't belong there and Neytiri can't claim all of Pandora.
So on the day Spider finds out he can breath Pandorean air, he leaves. He leaves notes for the ones he cares about in his bed and gets out of dodge.