looking for anime movie about young boy and girl journeying through the desert
I'm looking for this anime movie I saw when I was about 9 or 10. I don't remember any kind of title or what channel it was on. It was on TV and it was probably some time around '99 or 2000 and it followed this young boy and girl, possibly brother and sister, on a journey. I remember they were a desert sort of place, for some reason they left their homeland, and they were traveling with other people on these floating boats/ships. Random things I remember is that the boy didn't have a shirt and he had some kind of weapon that was shaped like a tube. He loaded these little balls in it and shot it by pulling some kind of string or something at the bottom and they exploded. I think they were being pursued and I remember the boy getting into a battle and using the weapon,but he ended up getting hurt. I never saw the beginning or the end, but I saw a good portion of the middle. I remember thinking it was so cool and even though I'd never known what it was or what the full story was, the whole idea of the floating ships and things captivated me. I would love to see this if anyone could tell me what it is.