There are so many things to do in and around Tokyo. Public transit in Japan is perhaps the best in the world. So Tokyo is an easy jumping off place to really any where in the country. You can also do day trips or quick over night trips to many of the close areas around Tokyo like the following:
Tochigi (Nikko is a must see)
Kanagawa (Go check out Yokohama)
Chiba (Tokyo Disney and very close)
Mount Fuji (~2 hour train from Tokyo)
And with the Shinkansen, you can also do quick trips down to Kyoto, Nara, Hiroshima, and farther south.
If you are planning a trip to Japan, I would recommend not renting a car and getting the JR rail pass. Using the JR network, you can just about get everywhere. This gives you unlimited rides for 1-3 weeks, includes the Shinkansen, and is the affordable option. Additionally, if you don't speak Japanese, it makes getting around a little easier with ticketing. This needs to be planned before you visit though. You need to apply for it, then receive it in your home country and bring it with you. You can not get this while you are in Japan.
Additionally, when I visit Japan, I like to get either a WiFi hotspot or a Sim card. The hotspot is especially nice if you are with a group because everyone can just connect to the hotspot and you can keep it in your backpack while you are out each day. I historically have always just picked one up from the airport when I land, but it is also easy to order these before you leave for your trip so you don't need to hassle with it in Japan.
If you are planning your trip, I would highly recommend trying to book to overlap the cherry blossom season. Cherry blossoms bloom at different times in the country, so you can plan your trip accordingly as well. E.g. Southern Japan blooms sooner than Tokyo.
Shinjuku is the world's busiest railway station. Many people make jokes about getting lost in the station, but it actually is huge. Great jumping off point for all of Tokyo. If you can book a hotel near here, it will make travel pretty easy.
If you can't find something reasonable, then focus on finding something on the Yamanote line.
Shibuya crossing is fun to experience. Good place to grab a meal as well. When you visit Shibuya, I also like to see the Hachiko statue.
Visit the Pokemon Center in Sun Shine City
Lots of other interesting shops in this area
Speaking of Sun Shine City, it has my favorite observatory in the country. Dusk is a nice time to visit and to stay until its dark.
Ueno has beautiful cherry blossoms if you are there at the right time. It also has a good zoo and parks. I also have always enjoyed the walk from Ueno station to Akihabara. Lots of good shops along the way. Start from the Ueno station on the east side.
Akihabara is a great place for electronics and anime & manga
Hike Mount Takao. Its relatively easy to get there via the Chuo line, and has a beautiful hike up to great views of the surrounding area. If its clear, you can also see Mount Fuji. The chair lift is pretty fun to take as well.
Kichijoji has great shops and if you are riding the Chuo line, it may be an easy place to stop for lunch. Sunroad is right off the main station. There is a spot that you used to be able to stand where you could see 3 Mcdonalds within a 3 minute walk
If you keep going up the Chuo line, you can also stop at Mitaka for the Ghibli Museum which is close by
Another fun stop on the same Chuo line is Tachikawa. It has the Showa Memorial Park which is Tokyo's largest park. There are some outdoor art exhibits in the area of Tachikawa as well which are fun to walk around and see.
Harajuku is a Fashion center and lots of fun shops
Ginza is a great place for a meal or nicer shopping
If you get off on the Tokyo station, you can walk to the Imperial gardens and see the Imperial Palace.
Tokyo Tower is visible from many different areas. You do not necessarily need to go to the base.
Yoyogi park is a beautiful park near Harajuku
Visit and eat sushi in the fish markets at Tsukiji. Some of the best sushi you will find.
Ramen Square in Tachikawa. It has a dozen shops that are routinely rated and if they aren't good enough, then a different shop comes in. Great place to see lots of different kinds of Ramen.
Street food is awesome in Japan. If you see chicken on skewers (Yakitori), then I would buy a few to try.
Fresh melon pan can be found at many bakeries
7/11s have great food. They are a great stop while you are out. Try the Nikuman.
Try some Gyudon from Matsuya, Yoshinoya, or Sukiya. I like Sukiya a little more than the others. Its not on the menu, but you can also get things in "King Size" portions which is very large.
If you are at an outdoor market, definitely get some Takoyaki to try.
Japanese curry is unique. Coco Curry is one of my favorites.
My favorite Japanese food is Sukiyaki. Many Shabu Shabu places will also have Sukiyaki.
Japanese Yaki Niku is also great. Stamina Taro is one of my favorites. There are multiple locations.
Tonkatsu is great and is all over. Find a restaurant that serves it. My favorite places will also have a way where you grind your sesame fresh like Wagokoro in Ginza.
Okonomiyaki - I prefer Hiroshima style
Low to mid range sushi is superior to Sushi in the USA. Kaitenzushi is my favorite way to do it.
My absolute favorite Donut shop is Mister Donuts. They are in lots of train stations. Get the honey old fashioned!
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