The majority of our tours start and end in Tokyo, so you will need flights to and from Tokyo's Narita International Airport (NRT) or Tokyo Haneda Airport (HND).
The exceptions are the Hidden Japan and Kyushu Elements tours which start and finish in Kyoto for arrivals at and departures from Osaka Kansai Airport (KIX) and the Spirit of Honshu tour which starts in Tokyo and finishes in Kyoto. On any of these tours it is easy to arrange add-ons for extra time in Tokyo (or elsewhere) and for arrivals / departures in Tokyo.