Extracting knowledge from the A+ certification guide I'm studying from... It's a General Protection Fault. Based on my experience, it happens mostly when a program is out of RAM. That usually means physical RAM, though not having enough virtual memory can also lead to the problem. Considering that most games don't unload resources until they quit (which makes sense with Aquaria, as you'll switch to similar/same past maps often), they take up a lot of memory as you play. Eventually, they take so much memory that the system can't give them any more, and the game tries to access memory past its allocated addresses, and trigger a GPF. That's where the debugging comes in, though most people don't have the skills for debugging. (Though that's all my own theory...)
If you beat Mithala at the beginning of your game session, you shouldn't be out of memory. And you're missing out on some info at the end of the scene, so it's recommended that you go back and watch the cutscene (which you can only do by beating Mithala ...again).