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1. Meiji Jingu & Harajuku. This Shinto shrine is easy to reach from any parts of central Tokyo. Once you get off Harajuku station, it's just within walking distance. The shrine complex in the middle of the forest. When you walk through the great torii, you literally leave the hustle and bustle of Harajuku into the leafy forest under the shades tree canopies. You can head to my story in here.
2. Roppongi street walks. I had a good time walking around Roppongi; walking up the steps through the bridge along the footpath with cool street arts complemented by contemporary buildings surrounding the suburb. From down to top view, Roppongi displays contemporary arts; street arts, art installations at museums, Pixar exhibition and many more. This suburb is modern, clean and clearly making a statement as a hub of Japanese contemporary culture. At night it is a hub for classy and trendy bars and restaurants. 3. Mori Museum & Tokyo Observation Tower. When visiting the Mori Art Museum, you can also enjoy Tokyo from the observation tower. The museum is on the top floor where you can spend your time observing Tokyo if you're tired of the art exhibitions. Roppongi Hills Mori tower is the hub of a contemporary art museum as well as pop culture exhibitions. You can combine your visit with two or three activities in one go. As for Tokyo Sky Tree is more touristy and its attraction is mainly the glass skywalk and modern shops and cafes on the lower levels. 4. Tsukiji Market: Eat, Have a Sit, Explore Start your morning at outer Tsukiji market. Firstly, enjoy your coffee at Honshi coffee before you start exploring the Tsukiji market with endless breakfast options from omelettes to grilled seafood. It's one of the best market experiences in Japan. I didn't take a group tour, and I still had the best time exploring the market with vibrant laneway shops. Just drop by the street food stall selling the Japanese omelettes. The most popular one is the one with the queue, of course. Get yourself in line with everyone else. Choose a convenient spot to eat instead of eating while walking because when in Japan, do as the Japanese do! 5. Omoide Yokocho & Shinjuku Just before dark unfolds, head to Omoide Yokocho under the Shinjuku Railway lines. Let yourself lost in the alleyways. Smell the Yakitori from their charcoal BBQ, join and squeeze yourself in one of their stalls to have Yakitori to your likings. Toss your beer pints to your next neighbour and say 'Kanpai!'
As the dark falls, make yourself cross the street under the JR railway bridge and bask in the light of Shinjuku. From this point, the options are all yours. Just keep up with your instinct, and you'll indulge in the Shinjuku nightlife.