I'm looking for an animated movie for kids. I watched it sometime between 2002-2005.
The movie starts with two kids/teenagers in a small boat. They find this chest containing a letter and I think there also was a crystal ball. (I'm pretty sure they found it in the ocean). Then the story goes back to the past where we see the writer of the letter who is a girl in her late teens/early twenties. I remember her talking to a man who I think was some kind of professor, and then she joined some people in a submarine (I'm not 100% sure of this, could also be a ship). I also remember a room in this submarine/ship with a large map.

I have tried looking for this movie for days but can't find it. So I really hope anyone can help me.