Complex sentence: Shortly after arriving at the school, his new friends discover after a magical display in the dormitory community bath that he is actually male, though this comes as quite a shock to him despite him being aware of the physical differences between him and normal girls.
Split into simpler sentences: Shortly after arriving at the school, his new friends discover after a magical display in the dormitory community bath that he is male. This comes as quite a shock to him despite knowing of the physical differences between him and normal girls.