As mentioned above, if you are interested in travelling around the country by train, take a look at the following website:
JR Rail Pass. You can purchase it before you come or after you arrive if you have a tourist visa.
There are also night buses that leave from Mito and go to areas like Kyoto or up north. Other night buses from Tokyo go all over Japan. Traveling around Japan is quite easy and many interns have traveled with each other.
The local airport also offers flights to areas in Japan for a reasonable price:
Ibaraki Airport.
Ferry service is also available for those wishing to travel to Hokkaido:
Sunflower Ferry.