A secret conversation can be witnessed in Metroid Fusion. To hear it, Samus must perform a difficult series of Shinesparks in Sector 4 after she has opened Level 4 security doors, but before she obtains the Diffusion Missiles.

Remember, the X and Metroids are "natural" enemies. In Fusion, the SA-X was willing to die in order to destroy the Metroid lab and an X core willing to blow up BSL along itself. Later, a SA-X "saved" Samus from the Omega Metroid which in reality was just a self-preservation method.

^ Adam: You know that the X reproduce by asexual division. Because of this mechanism, there are now no fewer than 10 SA-X aboard the station. Nintendo R&D1. Metroid Fusion.

Metroid Fusion is overtly a horror game, trapping Samus in a claustrophobic research station where all life (including other humans) has been eradicated and replaced by parasites capable of exaggerating their shapeshifting forms.