Tokyo station is the main station of Tokyo but actually it is not the busiest station in Japan. The busiest station with highest number of ridership is Shinjuku station in Tokyo. Probably you will think the second busiest station is Tokyo station, but it is not true either.
Tokyo station was the third busiest station of JR East in 2019. Roughly 0.9 million persons use the station daily. However, this number is just the passengers who used JR East trains.
If you consider private railways such as Tokyu or Tobu and subways including Tokyo Metro, Tokyo station is the sixth busiest station in Japan. Total daily ridership is 1.2 million.
Anyway, Tokyo station is the place where your journey in Japan by trains start.
You can take direct trains - Shinkansen to even to Hokkaido and Kyushu. Unfortunately Shikoku is not connected by Shinkansen, therefore you need to change at Okayama station on Sanyo Shinkansen. All Shinkansen trains except Kyushu Shinkansen depart from Tokyo station.
However, you have to remember which Shinkansen to take. If you are heading to Hakone, Nagoya, Kyoto, Osaka, Shikoku, Hiroshima or Kyushu, take Tokaido and Sanyo Shinkansen which is mentioned in blue icon. Then, if you are heading to Hokkaido, Sendai, Akita, Yamagata, Niigata, Nagano or Kanazawa, take Tohoku, Hokkaido, Akita, Yamagata, Joetsu or Hokuriku Shinkansen which is mentioned in green icon.