>>721107046
Humans still exist but in the first three zero games they're in neo arcadia which is considered a paradise for humans but a shithole for reploids, that's why the resistance exist was led by Ciel.

After MMZ3 Weil takes over makes it a shitty place for everyone so all the humans who are able decide to escape, it's also the first time in zero you see other humans besides ciel. They resent Zero and blame him for being the reason why everything goes to shit for them but eventually realize Zero isn't the bad guy and start to appreciate him