Not exactly Emperor vs. Shogun

From Samurai Revolution: The Dawn of Modern Japan Seen Through the Eyes of the Shogun's Last Samurai, by Romulus Hillsborough (Tuttle, 2014), Kindle pp. 92-94:

The Imperial Loyalists hailed from samurai clans throughout the country. Most prominent among them were Mito in the east, Fukui in the west, and Satsuma, Chōshū, Tosa, and Kumamoto in the outlying southwestern regions. Many of them were low-ranking samurai from the bottom rungs of their respective clans—and therein lay their superiority as leaders and as men. Generally, the lower-samurai did not have a voice in the policies of their han. They had to struggle, and often risk their lives, just to be heard. As a result, they were naturally more capable than the spoiled, privileged, and, more often than not, inept sons of the upper-samurai—a fact of which Katsu Kaishū was acutely aware. During times of tranquility and peace, the lower-samurai had been willing to accept their humble positions; but after Perry they demanded attention. Some left their han without permission to band together with Loyalists from feudal domains throughout Japan. In thus abandoning their han they became rōnin. (The term rōnin was used interchangeably with the less derogatory rōshi. The rō of both terms means “wave”—the gist being “wandering aimlessly.” The nin of rōnin simply means “person,” while the shi of rōshi means “samurai.”)

In former times, rōnin were merely lordless samurai—men of the warrior class who had become separated from feudal lord and clan. But after Perry, the term rōnin took on a much different connotation. Most of the latter-day rōnin were renegade samurai, political outlaws, who had intentionally quit the service of their lord and clan. Far greater in number than their predecessors, these men did not necessarily derive from the samurai caste. Some hailed from peasant households, and some from merchant families. And some samurai who technically became rōnin did not really abandon their daimyo; rather they quit their lord’s service in order to protect him from being associated with their own seditious activities. Imperial Loyalism encompassed a wide sphere extending beyond the anti-Bakufu and anti-foreign parties, and even the samurai class itself. Morals in Japanese society were based, in part, on the relationship between the sovereign and his subjects. The Emperor was sovereign. His ancestors had ruled in ancient times, long before the advent of the shōguns or, for that matter, any of the feudal lords. The people were the Emperor’s subjects—and counted among the Imperial subjects was the shōgun himself, who had merely been commissioned by the Emperor to rule.

The coming revolution, then, would not simply be a struggle between Imperial Loyalists on one side and the Bakufu and its supporters on the other. As already noted, most of the people who supported the Bakufu also revered the Emperor, and among those who swore absolute loyalty to the Emperor were some of the most devout Bakufu supporters. This dichotomy existed among individuals and groups alike.