While the Japan Rail (JR) Pass provides incredible access to the nationwide JR network, it is not a "universal" pass for all transport in Japan. It covers all JR-operated trains, including the majority of Shinkansen (Bullet Trains), but it explicitly excludes the fastest Nozomi and Mizuho trains unless you purchase a specific supplemental "Nozomi/Mizuho" ticket. Additionally, the JR Pass is generally not valid on private railway lines (such as Odakyu, Kintetsu, or Keihan) or the subway systems in cities like Tokyo, Kyoto, and Osaka, which are usually operated by municipal governments. While it covers some JR-operated buses and the Miyajima Ferry, you will still need a separate IC card (like Suica or ICOCA) to navigate local city transit. The pass is best used for long-distance travel between regions; once you arrive at your destination, you will frequently find yourself using non-JR lines that require separate payment.