Imperial palace is located in the very center of Tokyo, at the former Edo castle which all shoguns from Tokugawa Shogunate resided.
After Yoshinobu Tokugawa abolished the status of shogunate and returned the power to royal family, the emperor changed the seat from Kyoto to Tokyo. During the Tokugawa Shogunate, Japan had two capitals. Nominal capital, Kyoto and Edo(Tokyo) which was de facto.
There are 13 subways running through the city of Tokyo but none of them are running below the imperial palace which area is 1150000 m2.
There are two daily tours at the imperial palace which is commencing in the morning and the afternoon but limited to 300 persons each. Also East garden(HIgashigyoen) can be visited individually without any reservation but please watch out that Monday and Friday are closed except these days are public holidays. Also, you will get a plastic ticket at the gate which you have to return when you are getting out, therefore please do not lose it during your stay in imperial palace!