Day 1 (Tokyo):
-Checked into Imano Tokyo Hostel
-Dinner/drinks in Shinjuku Omoide Yokocho ("Piss Alley," lots of tiny bars and yakitori joints)
Day 2 (Tokyo):
-Tsukiji Fish Market (good to do on your first morning when you're super jetlagged, since you're supposed to go super early)
-I meant to go to Shinjuku Gyoen National Park this day, but it was closed over the winter holidays when I was there
-Gundam statue (not sure if it's still there, but it was in Odaiba near the Science museum)
-National Museum of Emerging Science and Innovation Miraikan (they have ASIMO!!!)
-Harajuku District/Takeshita Street
-Owl Cafe
-Shibuya Crossing
Day 3 (Tokyo):
-Watched sumo practice at Arashio-Beya Sumo Stable (http://arashio.net/tour_e.html)
-Cup Noodles Museum (Yokohama)
-Lunch at Ichiran
-Ginza district (shopping, Tokyu Hands store)
-Golden Gai (bars, restaurants, arcades)
-Robot Restaurant (buy tickets in advance, drinks and show only. Food is apparently terrible)
Day 4 (Hakone):
-Took train to Hakone (bought 2-day Hakone Free Pass at Shinjuku Station)
-Checked into Mount View Hakone (ryokan-style onsen hotel with single rooms available)
-Hakone Open Air Museum (sculpture museum)
-Museum of The Little Prince
-Onsen time (hot spring bath, shared but separated by gender)
Day 5 (Tokyo):
-Train back to Tokyo
-Checked into Kaisu Hostel
-Meiji Jingu Shrine
-Couchsurfing meetup (met really cool travelers and locals, went out for karaoke!)
Day 6 (Tokyo):
-Tokyo Skytree
-Lunch at Toriton Kaiten Sushi (conveyor belt sushi at Skytree)
-Senso-ji Shrine (for New Year's Eve)
Day 7 (Tokyo):
-Akihabara (tons of arcades)
-Namjatown "theme park" inside Sunshine City (fun but would not recommend if not accompanied by someone who speaks Japanese. I luckily met people who were there teaching English.)
-Pachinko (I would have never known what to do if I hadn't been with a Japanese speaker. I won some yen!)
Day 8 (Kyoto):
-Take Shinkansen to Kyoto (activated my pre-purchased 7-day JR pass. Make sure you buy an "ekiben" for the trip!)
-Checked into Piece Hostel Sanjo (the nicest hostel I have been to in the entire world!!!)
-Pontocho Alley
-Gion District
Day 9 (Kyoto):
-Arashiyama Monkey Park
-Arashiyama Bamboo Forest
-Kinkaku-ji Temple (Golden Pavillion)
-Nishiki Market
Day 10 (Kyoto/Nara):
-Nara Park (this is an easy half-day trip, but I was hung over, so this is all I did that day. Don't ever try to keep up with Australians!)
-Lunch at Marugame Seimen (chain, but amazing udon)
Day 11 (Kyoto/Osaka):
-Fushimi Inari Taisha Shrine (you don't have to do the whole way up; I'm told there's nothing special at the top)
-Travel to Osaka (easy for a half day trip)
-Osaka Castle
-Dotonbori
Day 12 (Nagano):
-Shinkansen/trains to Yudanaka (Kyoto > Kanazawa > Nagano > Yudanaka)
-Check into Senshinkan Matsuya (ryokan in an onsen village)
-Visit the local onsen (way hotter than I could handle)
Day 13 (Nagano/Tokyo):
-Jigokudani Snow Monkey Park (this is the whole reason I came up this way and it was worth it!)
-Train back to Tokyo
-Check into Akihabara Bay Hotel (female-only capsule hotel)
-Enjoy last night of Akihabara arcades
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