Actually, the Emperor wasn't significant during the Edo, mostly - it was ceremonial. He was there in Kyoto as cultural, historical significant figure in a way for a huge majority of the time. Here's a little history from before the Meiji, from what I remember, about the Court. Note: This is a really abridged history that's a mixture of readings from William Wayne Farris's Japan to 1600 and James L. McClain's Japan: A Modern History and lectures from my professor at college. I'm not really doing the Heian, Kamakura, Muromachi, Warring States, Edo and Meiji period any justice with this, but I hope it provides some background.

The court had faced a decline since the Heian period. The Heian could be said to be the last period prior to the Meiji where the court actually did play a big role in politics and government. They had a trifunctional elite already by the Heian - Warriors, imperial Court, and clergy. But, the warriors increasingly gained more power, became more prevalent in the elites and reached their heights with the Kamakura and the fall of Heian. The imperial court also lost some legitimacy with the Northern/Southern Court split during the beginning of the Muromachi period.

Beginning with the Kamakura bakufu to the Edo Period, the bakufu, and later, bakuhan system. The emperor was mostly a ceremonial figure, with no significance. In fact, the imperial family/aristocrats were actually quite impoverished during these bakufu times. Much of the politics, in fact, it's easy to say almost all, was in large part carried out by the bakufu and the Han (local domains that's part of the bakuhan system evident in the Edo period). Foreign and internal policy... mostly the bakufu.

Now, onto the Meiji. The bakuhan system was highly decentralized. An overarching bakufu and Han domain that had quite a bit of local autonomy. The bakufu had the superior authority, and they used most of it to keep the domains checked, to avoid a repeat of the Warring States period. But, that decentralization was what drove a lot of people to believe that the bakufu wasn't capable of reforming the country and helping the country through "naiyu gaikan" or "troubles within and without". The people believed that there was widespread internal and external crisis throughout the latter half of the Edo or Bakumatsu (fall of the bakufu). This is caused by a variety of factors - depleted natural resources, increased impoverishment of the warrior class compared to other rising classes like merchants, famines, riots... and more. External crisis includes rising Western influence from Russia, Britain, France, and of course America. But, even before America's arrival, there was the Opium War, major influence, that gave Japan a glimpse of a future if they don't react accordingly. The crisis became even more urgent with that event. They didn't ant to end up like China. The Ansei treaties (opening up Japan to Westerners) only fueled things. Most of Japan wanted to stay isolationist. Even Ii Naosuke, the one who signed the treaties, hinted that his ultimate goal was only to strengthen Japan before closing it to Westerners with stronger defense.

Now... notice... throughout my whole post about the urgency and crisis in the Edo... the Emperor wasn't involved. Because, he really didn't have any political influence during this time. The reason why the factions or the domains backed him is actually because of the shishi or radical activists, who were these people in unstable places in society (lessening their ties to the current status quo) who supported this saying, "Sonno Joi" or Revere Emperor, Expel Barbarians (fun fact, Joi is still used in Japan today according to a TA). They thought that the only way to get their country through these times with expanding Western power. They wanted a more unified government and they looked back at none other than the Heian period with peace and strong, centralized government. The fact that the emperor supposedly was a descent of god, this Heavenly Sovereign, which fueled some nationalism throughout the people. It was really just a source of nationalism, pride, and idea for conspirators to back the Emperor and think of Japan as this... heavenly state. Major conspirators, like the Choshu and Satsuma domain were always against the Tokugawa (they were part of the Tozama daimyo or outsiders) and I can't exactly tell you much about their alliance since it's not really within my knowledge.

Here's an argument about the Meiji Restoration - it isn't a restoration, it's a revolution disguised as a restoration that's going to be a common trend in history (a cover of "going back" in history, when in reality it's a leap forward. This "honor the emperor" was really a disguise for greater political, social change in the era after in Japanese history. The emperor, much of this time, played no role other than maybe conspiring with supporters (this I can't even find in my book from McClain to be honest), to overthrow the government. Much of this was actually other people in play.

Wellllll, I went off on a rant. But, credit goes to the two books named in the first paragraph and my professor from college. It's highly abridged.