Nice job!
This is a nice, solid RPG. Here are my thoughts on the graphics, sound, and gameplay:
Graphics: really nice! The whales and icebergs drifting past during on-ship combat were a great touch. I especially love the hand-drawn style, though I thought the speech bubbles looked a little wonky, and the water in the beginning looked just slightly radioactive. :-)
Sound: not bad. The sound effects were generic, but they did the job. The music was generally pretty nice, though I found the battle music repetitive and not entirely appropriate (the boss music was a little better). Also, a hint: import your tracks to the library as .wav files and let flash convert them to mp3 itself to avoid that little pause at the end of the track where it's supposed to loop.
Gameplay: generic RPG battles with a single character, and no control over your character's advancement (either skill-wise or plot-wise). Clearly there's not a whole lot of versatility here, but for what it is, it's well-done. I don't know what your plans are for the next chapter (and indeed, you say it's already nearly done), but if you haven't already done so, I recommend adding in a greater variety of abilities, other characters, and/or a more flexible system of advancement. Any of these would boost the interest level of the gameplay considerably.
Anyway, good work, and I look forward to seeing how this series progresses. :-)