So Why Does Roxas THINK He Left the Organization?

But hell, that's how he started out as a Nobody. That could be exactly why he left, because the other Nobodies remember their previous life and show no interest in his lack of memories. All he knew (or at least assumed) was that he was special and that no one else seemed to care, thus he left to figure it out. Assuming that he suspected someone tampered with his memories, there's very little evidence that the rest of the Org is innocent in that so why would he trust them, let alone stay with them?

 

But he started off like that, now it'd be uneven. There's basically jsut be huge inexplicable, yet weirdly specific gaps in his memory
And also, why would he care about the keyblade or know about Sora WITHOUT memories of Xion to contextualize them

 

Or, he could remember he did some stuff but not with whom. And that he used to hang out on the clocktower a lot with Axel and... wait, was there somebody else? I could've sworn... Nah, I dunno who I was thinking of.

You act like there's no context to anything he did ever just because one person got zapped from his memory—and that memories are rock-solid, and missing pieces are like sirens going off in your head. That's not even slightly how memories work and simple reflection on your own brain should tell you that. Memories might be the fuzziest damn thing on the planet. They go missing. A lot. We don't question it. If we did, we'd all be nervous wrecks.

 

It's kidna a big deal when that ONE person is the focal point of nearly all your memories
Days showed us, Roxas didn't have a whole lot of variety in his life, pretty much all of it was about Xion on some level, worrying about her, chatting with her, worrying about her, eating ice cream with her, worrying about not eating ice cream with her
Sure, in real life removing one person probably wouldn't be as big of a deal, but there are only three people Roxas had any significant interaction with in his ENTIRE life

 

So what's left when you remove her?

"Axel's cool. Saïx is a jerk. That Xigbar guy tried to kill me once, that sucked. Everybody else here is creepy and weird. And Xemnas is just a son of a b██ch. This place sucks."

Sounds like good enough reason to leave to me. (Note that there has been a change there, at the start his attitude was "Who are you people")