Before he was off'ed, Yamamoto was planning to trap part of the U.S. fleet in the Atlantic by bombing the Panama Canal.
A special twin hulled sub, the 1-400, was built to launch 3 airplanes for that task, and bomb coastal cities and refineries at night.
I-400 class submarine - Wikipedia, the free encyclopedia
With Yamamoto gone, the Army delayed the program until well after the Asian theatre was under way. It was then suggested to use the submarines for germ warfare against the west coast cities using the I-400 or ballons, but the idea was nixed. Some Japanese general said this would start "a war against humanity".
The chains of islands leading to Japan were conquored because the defenders often lacked resources. The central planners always had the final defense of the home islands in mind, and a conventional invasion would have taken years, if successful. Air superiority would have allowed carpet bombing of military sites, but a ground war would have been brutal(aka vietnam).