The space pirates may know Samus as the Hunter, but as far as the X-Parasites are concerned, shes the most dangerous metroid and refer to her as such.
I'm pretty sure it's the Samus clone.
oh great, this means they probably set up an ambush in the Chozo temple that Samus has to go to to get a new suit. Thats being optimistic, the worst case senario is they simply destroyed it or corrupted it in some way.
If you've played Metroid: Prime, you'll know they didn't destroy it, otherwise there wouldn't have been any left to come make the report. As for corrupting it, the only way they could do that is if they infect it. All that has to happen then is Crono uses his sword Techs to force the infected aspects to revert to X form, at which point Samus absorbs them.
If an ambush, then the Temple will protect Samus once she gets there, as she will be veiwed as a visitor, as opposed to the SA-X's, who are trespassers. Not to mention the fact that she's accompanied by a native (Crono) who has played a significant role in several points in the timeline.
I guess we aren't finding out if my plan worked quite yet...
The Pirate call her the Hunter, the Parasites call her the Metroid...MAN the badguys REALLY hate calling her by her ACTUAL NAME...