The best explanation of how Japan was organized politically during the medieval period is:
A network of warriors governed Japan at all levels, including the shogun, who was more powerful than the emperor.
During the medieval period in Japan, particularly the feudal era, the shogun held significant military and political power, often overshadowing the emperor, who was more of a symbolic figurehead. The samurai, as part of the warrior class, were vassals to the shogun and played crucial roles in governance and military service throughout the country.