Day One - I'd start at the Tsukiji Market. The wholesale area closed down in October 2018 but the area is still bustling with business the same as before. The neighborhood is full of action in the morning hours. There are many places to try sushi, so if you have not had breakfast yet, this is your chance. A 15 minute walk will take you to the Hamarikyu Gardens, a former duck hunting ground in the Edo era. Once you have enjoyed a stroll around the huge pond, you can hop onboard a river bus that will take you to the old district of Asakusa. The red paper lantern hanging on the Kaminari-mon Gate makes for a good photo - join the throng of other tourists who have gathered from all over Japan. The main passageway leading up to the Sensoji Temple has souvenir shops lined up on both sides. By now, it's late afternoon and you can ride the Tobu Railways for one station to the Tokyo Skytree, the tallest TV tower in the world at 634 metres for a view of the sunset. If the weather is lousy, you may want to choose to hop on the Subway instead and go straight to the Ginza district, which has always been the center of dining and shopping.
Day Two - Let's begin the morning at Meiji Shrine, dedicated the emperor that had a major part in Japan's modernization from the late 19th century to early 20th century. Once we have purified ourselves, it's back to the city as we walk the sidewalks of Omotesando, a posh shopping district, where all the brand names are. We continue onwards to the Tokyo Midtown/Roppongi Hills area, home to famous modern architecture such as the National Art Center by Kisho Kurokawa and the 21_21 Design Sight by Tadao Ando. By this time of the day, at Shibuya, the famous "scramble" intersection starts to get busy. You can watch it from the Starbucks steps away (always crowded) or from the covered ped crossway to the south. Once finished people-watching, depending on the weather, you can spend the afternoon at the Shinjuku Gyoen which has a mixture of English/French styled gardens or if the weather is not favorable you can familiate yourself with the history of the city by visiting the Edo Tokyo Museum.
Day Three - Start your day with a visit to the East Gardens of the Imperial Palace. Not much remains from the former Edo Castle so you'll need to use your imagination to connect with the past. Next, get on the Yamanote Line for Ueno, the "Museum Mile" of Tokyo. There are several museums and galleries to choose from, but the National Museum will give you a good understanding on the evolution of Japanese art. Continue north towards the old Yanaka district. Unlike other areas in Tokyo, Yanaka was able to avoid damages from the 1923 earthquake or the bombs of WWII. Finally, we shall enjoy the views from the fully automated Yurikamome Line via the Shimbashi terminal. The Yurikamome (meaning "Seagull") will give you a birds-eye view of Odaiba and the Tokyo Waterfront as it crosses the Rainbow Bridge. There is a replica of the Statue of Liberty, and other SF-like buildings in this district that was developed only in the last 20 years. You can dine here or opt to return to Shimbashi which is a favorite drinking place for the Japanese businessman.
Some info to keep in mind...
Many museums are closed on Mondays...The Imperial East Garden is closed Monday and Friday.
The trains are absolutely packed from about 7:30 to 9:30am on weekdays...try to minimize train travel during this period if you can...
Trains run until about midnight or up to 1am on some lines, but they don't run 24 hours. The first train is around 5 or 6am.
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