Tokyo Uncovered

Within Tokyo

Museum

NEZU Museum
http://www.nezu-muse.or.jp/en/index.html
Edo-Tokyo Museum
You can follow the transition of the city from Edo to Tokyo through exhibited artifacts and models both large and small. The exhibits include the castle and the daimyo (feudal lord) mansions, moat, store, and so on. There are also models of the Nihonbashi and Ryogokubashi bridges that reproduce the vitality of that time.
http://www.edo-tokyo-museum.or.jp/english/
Ukiyo-e Ota Memorial Museum of Art
This museum exhibits a large collection of ukiyo-e paintings and prints.
http://www.ukiyoe-ota-muse.jp/index-E.html

Historical sites: shrines, temples, etc.

Senso-ji
Senso-ji is an ancient Buddhist temple located in Asakusa, Taito-ku, Tokyo. It is the oldest temple in Tokyo. According to legend, a statue of the Kannon-Bosatsu (goddess of mercy) was found in 628 by two fishermen. The chief of their village recognized the sanctity of the statue and enshrined it. In 645, renowned Buddhist priest Shokai Shonin built the first temple. During the Edo period, the temple was protected by the Tokugawa shoguns after Tokugawa Ieyasu (first shogun of the Tokugawa shogunate) designated it as tutelary temple of the Tokugawa clan.
http://www.senso-ji.jp/about/index_e.html
Imperial Palace in Tokyo
The Imperial Palace in Tokyo is the residence of Japanese Emperor and is called Koukyo. There was once the Edo Caste during the Edo period (1603 - 1868), and the Tokugawa shoguns resided the castle. After the Meiji Restoration in 1868, Emperor Meiji moved to Tokyo from Koto.
Tokyo Imperial Palace Inner Grounds Walking Tour
Application: http://sankan.kunaicho.go.jp/english/index.html
Leaflet: http://www.kunaicho.go.jp/e-kunaicho/leaflet.html

Stores / Malls

Aqua City
http://www.aquacity.jp/en/top
Ame-ya Yoko-cho Market
http://www.ameyoko.net/e/
Tsukiji Market
The Tsukiji market is one of Tokyo Metropolitan Central Wholesale Markets, which handles the largest volume of marine products in the world.
http://www.tsukiji.or.jp/english/
Tuna Auction Watching:
Visitors can observe tuna auctions from a designated area. The number of visitors to tuna auctions is restricted to 140 per day on a first-come, first-served basis. Registration begins from 4:30 AM on the first floor of “Osakana Fukyu Center” located next to the Kachidokimon Gate.

Nature & Others

Mt. Takao
Mount Takao is a mountain in the city of Hachioji, Tokyo (located about 50 km from the center of Tokyo) with elevation of 599 meters (1,965 ft). It is a popular hiking spot with eight courses. The 2007 edition of Michelin's Voyager Pratique Japon, the famous French travel guidebook, awarded Mt. Takao the maximum of three stars. The mountain is one of must-see sightseeing spots in Japan.
http://www.takaotozan.co.jp/takaotozan_eng1/index2.htm
Tokyo Tower
http://www.tokyotower.co.jp/english/
TOKYO SKY TREE
http://www.tokyo-skytree.jp/english/

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Outside of Tokyo

Kawagoe, Saitama Prefecture

Kawagoe is a town of history retaining the culture and aroma of Edo, being away only 30 minutes by train from central Tokyo. Kawagoe is called “Koedo,” meaning a town like Edo (a little Edo.)
http://koedokawagoe.com/internacional/pg_englishu.html

Mt. Fuji

Mt. Fuji is the highest mountain in Japan at 3776 meters (12389 Ft.) The mountain has a nearly perfect conical shape and people worshiped as a sacred mountain. Mt. Fuji has attracted not only Japanese, but also foreign climbers. The ascent to the summit does not pose major difficulties regarding climbing skills. However, climbing Mt. Fuji is dangerous, and it could be fatal to you even in summer. You need to well prepare for sudden or extreme changes in the weather.*