Samus IS a GirlShe just pretends to be a guy so that Qwaritch would not have sex with her.
The whole story is Quaritch's Dying DreamAs Quaritch dies in the cockpit of his AMP suit, with two huge arrows poking out of his chest and poison running through his systems, he has one last dream/hallucination in which he imagines what would happen if he got out of his predicament. The spelling errors, poor grammar and ridiculous, non-nonsensical plot points are all results of poison from the arrowheads running through his systems. At first, he's hell-bent on revenge, but then he starts to regret what he did, which explains the abrupt HeelFace Turn. Oh, and the whole "have sex with hot Navi hoes" angle comes from his deeply suppressed attraction to the Na'vi.
These stories are actually based on rejected drafts for a script for an actual sequel to AvatarBut James Cameron hated them so much that he threw them out of a window. The author of these Fanfictions randomly found the drafts and decided to make a (horribly flawed, yet very entertaining) story out of it all. And, as they say, the rest is history.