A perfectly paced itinerary when looking at the locations you travel to, as well as the amount of activeness that is included. You have the opportunity to go beneath the surface of Japan by getting off the beaten track, and also having the exclusive and unique opportunity to mingle and talk to the locals in their rural home. Nothing better than to have a citrus aroma bath and then a meal at a Japanese home.

Day One (Tokyo)

Welcome to Tokyo & Japan!
After your immigration and custom formalities are complete, you will be met by your English Speaking Assistant and then transfer to your hotel in central Tokyo. You will be using the Green Class Seats on the Narita Express Train. (Or Local trains if you arrive into Haneda International Airport).
(Example Accommodation : The Peninsula Tokyo Hotel) 

Day Two (Tokyo)

Meet with your English Speaking Guide and commence Tokyo sightseeing by Public Transport. (Public Transportation such as the Local Trains, Subways and Buses will need to be paid on the spot) . Visit the Tsukiji Fish Market first to walk the outer market area. This is great for Foodies. Among other sightseeing is SENSOJI, also known as Asakusa Kannon Temple, Tokyo’s most colorful and popular temples. The Tokyo Sky Tree Tower is also walking distance from Asakusa. Visit the trendy and popular Shibuya area and try your luck crossing the scrambled crossing with all the other 2000 people at one time. Also visit Akihabara area to satisfy some of your Anime needs as well as the electronic paradise.
(Example Accommodation : The Peninsula Tokyo Hotel) 

Day Three (Tokyo)

Today is a Full Free day at leisure. Sleep in to your hearts content, and then walk the local streets and explore. Some suggestions would be ; 
● Meiji Jingu Shrine
● Harajuku
● Daikanyama and Omote-Sando areas
● The Imperial Palace, and more. 
(Example Accommodation : The Peninsula Tokyo Hotel) 

Day Four (Tokyo – Hakone)

Transfer from Tokyo to Hakone by the Bullet Train (Green(First) Class seats) with an English Speaking Guide to show you the sights of Hakone and how to make the most of the Hot Springs.  You will have the Hakone 2 day pass to cover all transportation and activities while you are in Hakone. Take the unique zig-zag train from Yumoto Hakone to Gora and see the Open air museum if you are interested, along with taking the Cable Car and Ropeway to Ohwakudani Thermal area and then to Lake Ashi with magnificent views of Mr Fuji. Relax at your hotel, and take in the amazing natural atmosphere along with your private Hot Springs bath.  
(Example Accomodation : Gora Hanaougi Ryokan : Japanese-Western Style (With private Hot Springs Bath))

Day Five (Hakone – Kyoto)

Depart your Hotel and transfer to Odawara Station. From Odawara Station, take the Bullet Train(Green (First) Class seats) to the City of Kyoto. Upon arrival at the station, meet with an English Speaking Assistant and I suggest you take a taxi ride from the Station to your Hotel. 
(Example Accommodation : The Ritz Carlton Kyoto Hotel)

Day Six (Kyoto)

Today is an introduction to Japans Capitol of Culture and Tradition, Kyoto. Travel by a Private Car and English Speaking Guide. First you will be taken to a World Heritage Temple in the mountain area of Kyoto. This Temple was the first location ANIME was drawn by the monks here. Go early and you will have the World Heritage site to yourself. Then take a 16km traditional Japanese boat ride d own a spectacular river to Arashiyama. Visit the famous Bamboo forest. Also visit, the Golden Pavilion, Nijo Castle. Walk the Nishiki Markets which have sustained Kyoto residents for some 400 years. 
(Example Accommodation : The Ritz Carlton Kyoto Hotel)

Day Seven (Kyoto)

Today you will be using a Private Car and and English Speaking Guide to take you to the outskirts of Kyoto, and away from the hustle and bustle of the central City. Arrive and see the two special Shrines before you take in a very special lunch. You will be sitting over a flowing river on Japanese Tatami mats which will be possibly 5-10 degrees Celsius cooler than central Kyoto. The presentation of the traditional Japanese lunch is impressive. Transfer to central Kyoto and visit the Famous Kiyomizu Temple – which uses not even one nail in its creation and of course a World Heritage location. Last stop, Sanjusangendo Temple which is the longest wooden structure in Japan, holding 1001 gold Buddha Statues. 
(Example Accommodation : The Ritz Carlton Kyoto Hotel)

Day Eight (Kyoto)

Use a Private Car to take you into the mountain area of Kyoto. A day to remember and an unique / exclusive experience. Walk part of the Kyoto Trail along a special river. Then take the steep route up a sacred mountain to a shrine at the summit (937 m) – a hike with a goal and much spiritual power to be gained by stepping foot into the Shrine. (the Shrines name will be advised after the booking is made ). Then take another route down to a citrus producing village. Here you will be invited into a local Japanese house and have a regional style lunch. Before the lunch you will have the chance to enjoy a bath at the local house which will have some of the locally produced fruit floating in the bath with a great aroma. Mingle with some locals and then return to Kyoto. 
(Example Accommodation : The Ritz Carlton Kyoto Hotel)

Day Nine (Kyoto)

Today can be a relaxed day in Kyoto, free at leisure. Kyoto is a marvel at merging the modern trends with the traditions of Kyoto. Walk the central streets of Kyoto and see how Kyoto people spend their days. 
OR if you want some more sightseeing, you may like a day tour to OSAKA, Japans second largest city and only 35 minutes from Kyoto. 
OR you can take a day tour to NARA city which was the Capitol of Japan be fore Kyoto (from the year 710). 
(Example Accommodation : The Ritz Carlton Kyoto Hotel)

Day Ten (Kyoto – Tokyo Airport)

Take the Bullet Train (Green(First) Class seats) to Tokyo. You may like to buy some snacks or lunch and eat while on the Bullet Train. 
Arrive at Tokyo Station and meet your English Assistant. You will then change to the Narita Express Rapid Train and transfer to Narita Airport with the Assistant.