Could the United States have actually taken over the country if they refused to open itself up to Western trade? Did the United States have the resources to do this? And if so, was there enough political will to make it happen? What was the plan if Japan continued to isolate itself, despite Perry's ultimatum?
Hey, a topic I've read primary sources and am familiar with!
It depends somewhat on how you refer to "take over the country", but while they could have caused really serious problems for Japan I'm inclined to disagree with some of the other posters and say no.
While Perry's ships were waaaay ahead of Japanese naval technology, in the end they were still only a single naval fleet. Perry didn't have much ability to project force far inland, and only carried a few hundred marines (about 250 on his first visit, and 500 on the second the following year). And on land there was less of a gap between the Japanese and the Americans. Contrary to popular image, the Japanese had possessed muskets and some small cannons for hundreds of years by the time Perry came. Even if the Americans did have more modern equipment and tactics, they would have become seriously outnumbered and outgunned as soon as they moved far enough inland their ships couldn't support them. The Japanese had also been isolated for so long that usual naval tactics like a blockade would have been of limited effect against them.
Even if the US fully pushed all their might behind the effort, it might have still been difficult just due to the difficulties of trying to resupply troops across the Pacific in an area with no friendly ports. That was still difficult in WWII, with much much better naval equipment. So "taking over the country" was impractical.
That said, "taking over the country" was never their goal, or even really threatened. IIRC the biggest threat Perry ever hung over the heads of the Japanese delegation was to take his ships up to Edo (modern day Tokyo) and march his marines to meet and negotiate with the Shogun in person. That was a terrifying prospect for the Japanese- not only was the current shogun literally on his deathbed (he died right after Perry finished his first visit, and was succeeded by his very young son), but it would catastrophically reveal how weak the shogunate was. They were under an order not to allow any foreigners on Japanese soil, but they were pretty much powerless to do anything to Perry and his delegation. Even just negotiating with Perry was enough to leave to the shogunate being overthrown a few years later. It would have been much worse if they marched through the capital and into the palace while officials were unable to do a thing about it.
Perry's expedition was there to negotiate a treaty. They weren't going to take no for an answer, but they were still there for a treaty and not a war.
I don't know if there were ever any plans for what would be done if Perry failed. In certain ways Perry's fleet was the backup plan. There had been several attempts to open Japan throughout the 19th century, and all had been brusquely turned away, with violence in some cases. James Glynn anchored in Nagasaki bay in 1849 to demand the return of some shipwrecked US sailors, and afterwards he was the one to recommend that any attempt to open Japan to trade be backed up with a show of force. Japan had already said no to negotiations several times. The whole point of Perry was to put them in a situation where they were forced to negotiate.
Honestly, I think it was extremely legitimate.
The reason that the approach caused such a huge panic was because the technology Commodore Perry brought and showed off was far out of Japan's league to deal with. I invite someone to correct me if I am wrong, but to my knowledge:
First: The U.S.S. Mississippi was the largest naval vessel most Japanese had ever seen. Up until that time, Japanese warships capped at about 18 to 19 meters. The Mississippi was 70 meters. Not feet; meters.
Second: These ships had armor- very imposing armor. This is actually not alien to the Japanese in and of itself; they had something called "Atakebune", notorious for having iron builds, some two-hundred years earlier. And those were often imagined in recounts as having iron plating- and were described as such by a Portugese priest in a letter- so it's only natural that many Japanese citizens envisioned such.
However, to my understanding, the Atakebune had been mostly decommissioned for a long time, after they were outclassed by the Korean Panokseon in a preceding war.
When Perry came over with his ships, many Japanese people were finally seeing a legendary armored ship for the first time- but as a potential foe, instead of as a means of defense.
Third: While I think most Japanese had seen steam ships come and go, the Black Smoke emitted by the Steam engines was immense, like nothing most Japanese had ever seen before. It was billows of smoke thicker than any safely-contained man-made fire (at least to their knowledge) could possibly emit, so dense and so large that if you hadn't seen the ships, you'd swear that whatever it's coming from couldn't possibly be safely, coherently functioning.
Yet that is what was the case. This smoke was coming from something that didn't seem harmed by it at all. Most could probably tell that that it was using that.
In my opinion, the psychological effect of this on Japanese witnesses probably compared well to the old horror movie trope of someone/something immolated with roaring flame continuing to walk and/or talk to the pending victim as if nothing is happening. Or, going much further back than that, of Dragons being able to breathe fire, projecting it from their very lungs. Hey, before Dragons were associated with fantasy, they were figures of horror.
Fourth: Lastly, this thing obviously outclassed the best the Japanese had in the way of weaponry. If I remember correctly, this thing hovered well out of the range of Japan's archers and was positioned to fire.
I apologize. I have just spent a substantial amount of time going on about why the Japanese felt worried about this, only to realize at this point that the answer you seek is far more... rigid.
I am very sorry about this. I'll make a separate post and attach my personal suggestions for answers to your actual questions there.