Great stuff, Gideon. I love the diversity in the game (well, it's not all that diverse, it's an RPG. But still, two different battle types, making certain party members have skills for their own puzzles and stuff, neat!).
However, I found a small text-related bug in Chapter 5, after you beat the boss:
There's a blank line there when it shouldn't be, the "'s" in "mission's" bleeds into the text box, and for god knows what reason, the "'s" part is reversed, too.