In the last comic, Prometheus mentioned getting past a psycho girly robot, which, of course, had a double meaning. The first was that Iris was apparently outside, while the other was referring to Zero and his part of the Cataclysm, and how if Proto Man is around in the future, he must have been able to survive Zero's time as a crazy girly robot.
This, then, explains why Prometheus says, "Not directly." when Zero asks if they're talking about him, because, well, they sort of are, but not directly.
And I like the idea of someone proclaiming that he's going to stand on the other side of the room acting indignant.