I think the Section 31 agent at the end of the comic is Number One. That's why we didn't see her face--it would have been recognizable. And it would be in keeping with the Ongoing comics to bring out cannon characters.
Hey, I wonder if they'll make a thing out of the fact that Number One looks a lot like Christine Chapel.
[A possible explanation for why Chapel "took a deep space assignment" was that she was maintaining her Section 31 cover and duties and that she is also Number One.]