Her Vagina

The AI decided to inject the Nanites into Samus's vagina to start it's experiments. These Nanites are purposefully built to be unstable, so there's o telling what would happen.

Ideas:

Engorged pussy: her pussy will become engorged.

Engorged pussy (Alt): her pussy will become engorged, and it will also grow hair in that area as well.

Penis Growth: a penis will sprout from her pussy.

stretchy: her privates can now stretch beyond human limitations.