Queen Neherenia has a completely different origin in the manga than she does in the anime. The manga Neherenia is evil, pure and simple, and not simply a lonely child. She considers herself to be the righteous Queen of the Moon and the Earth, and intends to destroy Elusion and the heirs of the Silver Millenium to get her due.

She first appears to Queen Serenity in the Moon Kingdom, during the ceremony to celebrate the birth of the princess. She is shrouded in shadows and everybody can tell she is evil. She complains she hasn't been invited, and reveals she lives in the depths of the moon. She had come there from nowhere, and nobody, to this day, had noticed. Queen Serenity assures her that if she came seeking peace, she was welcome, but that otherwise, she had to leave. Neherenia refused to leave, and offered Serenity to join with her, stating that light and darkness need each other and that Serenity, too, came from across the galaxy and that they weren't that different. Neherenia prepares to attack, glowing with power, but Queen Serenity is quicker and seals her in the silver crystal, and then in the mirrors, for Neherenia to forever be prisoner of her own darkness. Before she disappears completely, Neherenia presents the Queen with her "gift": a curse. Her curse was, soon, the kingdom would be destroyed and the princess would die before stepping on the throne (sounds familiar?).

For most of the Dream Arc, Neherenia stays behind her mirrors and after having put the spell on Helios and Elusion, she does little more than keep an eye on Elusion and its priest and give orders and instructions to Zirconia. That is, until Super SailorMoon follows Zirconia behind the mirrors and finds herself facing... Neherenia. The Queen of the Dead Moon does not put up much of a fight at that point, allowing Moon to free ChibiMoon and Saturn. She is defeated when the senshi break the mirror Moon followed Zirconia into.

But that is not the end for this Dark Queen. The mirror explodes, but she reappears in Elusion, and the real fight begins. She succeeds in taking the silver crystal away from Sailormoon.

In this moment of triumph, she says her curse is now going to be fully realized, and that both Elusion and the Silver Millenium will be totally destroyed. However, things go wrong and Neherenia's reign is among the shortest in history. Usagi and Mamoru kiss deeply and the silver crystal is returned to Usagi, whose Super SailorMoon fuku reappears. Without going into details, many things happen and Neherenia finds herself facing the new and improved Sailormoon: Eternal SailorMoon. The senshi send her their strength, also power up to their Star forms, and Eternal SailorMoon defeats Neherenia, who, dying, turns into something looking suspiciously similar to Zirconia before disappearing for good. Neherenia's season spanning privileges are anime only, so she stays dead.

Neherenia always stays behind her mirror or in Elusion, while Zirconia is never seen elsewhere than on this side of the mirror, so to speak. This, combined with how Neherenia looks when she is defeated, created one of the many...

[roll drums]
SAILOR MOON MYSTERIES.

[ahem]
Anyway, what I mean to say is, some people believe Zirconia and Neherenia are meant to be two aspects of the same entity, Neherenia being able to exist only in mirrors and in the land of dreams: Elusion, while Zirconia would be some kind of real world reflection of herself. They do talk to each other though, so whether or not they are two of the same, they are still somewhat distinct, at least as far as they know. This is completely opened to interpretation, and if someone tries to tell you that the manga clearly says this is true, they're wrong.