Well that's what my friend thought of the game, and here's my little theory on it...
We've all seen that the protagonist has an evil side to her, and she believes that she's the last one of her species. Well this is what I think: Her good side became unconscious and totally woke up her evil side. Her evil side wrecked havoc on the aquatic city and killed all/most of the civilians. And when her good side wakes up, she has no recollection of the bad deeds her evil side did.
Where did I get this idea? Well it wouldn't be the first time the "Good and Evil" aspect has been played in fiction. Just take a look at The Incredible Hulk, Dr. Jeckle and Mr. Hyde, and Dragon Ball (whenever a saiyan turns into monkey form).
-BGS