And this should clarify the fact that the two Samii are indeed different.

Oh, and if you didn't catch it... the ZR388 Samus is talking about when she was standing on the save point up near Metroid Queen's area.

Several minutes later
...So I'm standing on a pillar thing, when Kraid spontaneously disappears and I'm stuck at a dead end with some fake ground above me that I can't reach. Well, that pissed me off...
...So naturally, you need booze.
EXACTLY! So I wandered back here.
Which just confounds MY problem. Y'see, I didn't even know this bar EXISTED until an enemy showed me.
God, this place is screwed up. Wonder what happened.
Meanwhile, back on Zebeth...
Well... this is a whole assload of underwhelming. Boy, sure am glad I used those missiles on getting through the MYSTERY door!
Umm... crap. Hello? Anyone down there?

Metroid, Samus, Kraid, and the rest of 'em are all property of Nintendo, who to my knowledge wouldn't do anything such as sue me or shut poor Planet Zebeth down, because they're so damn nice, and Metroid kicks ass : }
This particular comic strip was made solely by me, by that happy little program known as KolourPaint. Yes, the one that everyone runs in fear from. That's why the comic looks the way it does.