Personally, I think the ending of
Godzilla 2000 is open to interpretation. Sure, it LOOKS like Godzilla is walking away victoriously after defeating Orga, but I think it's pretty obvious he was beating a hasty retreat before the Millennians sent reinforcements. Remember, they travel through space; just because we don't see them in the sky doesn't mean they're not flying above menacingly. I think if the film had lasted a couple minutes longer we would have seen Orga regenerate and finish him off. Chalk this one up as another draw for Godzilla, based on what we don't see happen.
Just my opinion.
