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This article is to help those who wish to travel from Tokyo to the Hakone area. The typical trip to this area is two days with one overnight (or perhaps two overnights). It is possible to visit here for a single but long day (this article was written based upon a single day visit).
The transportation system in the Hakone area is all tightly linked and coordinated amongst various trains, bus, cable trains and finally cable cars. Let's start by getting there from Tokyo. The Odakyu rail company offers direct service from Shinjuku main station direct to Hakone-yumoto (the beginning of the Hakone region). http://www.odakyu.jp/english/rc/index... This website is excellent and easy to understand.
The train runs regularly on what they call a "romancecar" service. The train is all reservation (meaning you need to book ahead) and utilizes some interesting looking trains and makes limited stops enroute. It's quite comfortable. Trains on the weekend can sell out. All romancecar trains leave from TRACK 2 from Shinjuku (enter on the West side of the station to get here quickly).
It is recommended to purchase your tickets in advance, the ticket counter is also found near TRACK 2 and listed as Odakyu ticket center, HOWEVER, go to the ticket counter (yellow signage) directly LEFT of the Odakyu ticket center. This is ticket center is run by Odakyu but the personnel speak English and focus on the romancecar service. They are quite helpful and will load you up with plenty of maps and ideas.
Total travel time is 80-90 minutes to Hakone-yumoto. The train ride is not spectacular nor high speed, as you're barely out of the Tokyo metro area.
Alternatives: You can purchase a standard ticket to Odawara and then change trains to continue on to Hakone-yumoto. This would likely save you a bit of money, but would take longer and if you're not familiar with how Japanese trains operate, you might get confused.
Things not to do: Several tourist bus run down in this area, however from Tokyo it's a long ugly bus ride and best avoided.
Travel tip: When making your return reservation, make it for the last possible return you'd like to take, if you wish to return earlier, you can change it at no cost at the Hakone-yumoto station (assuming seats are available).
The Freepass basically includes roundtrip from Tokyo to Hakone and virtually all transportation systems while in the Hakone area. It's a good value and a 'must purchase' if for nothing else to make your life easier as you roam about. The pass also offers various discounts at things along the way.
Departing Shinjuku station at 9:00 am, you'll arrive at Hakone-yumoto and it's best to press onward and upwards. Upon arrival, follow the crowd across the tracks to board the Hakone-Tozan train which runs approx every 20 minutes going to Gora (the last station).
The station prior to Gora is Chokokunomori and you should exit here (arriving at 11 a.m.) to visit the world famous open air museum (follow the directions it's a mere 10 minute walk). Plan to spend 1-2 hours at this museum and remember it's outside so skip if the weather is poor (saying that you may wish to skip the entire trip if the weather is poor).
Finishing the museum, there are a few quaint lunch places on the walk back to stop for a quick bite. You're heading to Gora next. If you have the energy, it's a 15-20 minute walk to Gora from Chokokunomori (just follow the main road, nearly impossible to get lost).
Gora is a better spot for lunch with more restaurants and here you will board the Cablecar which will drag you further up the mountain to a station where you will board the Hakone Ropeway which lifts you to the highest point of the mountain and from where (on a clear day) you will see Mt. Fuji.
It is suggested to exit the station (Owakundani) here as the next Ropeway is heading down. At Owakundani, you're as high as you're going to get and suggested to bring a warmer jacket and rain gear as the wind blows nearly constantly and it's indeed colder. Owakundani has tourist places to eat and don't miss the walk up to the boiling springs where for 500 Yen you can buy 5 eggs that have been boiled in the springs rendering the outside a dark black color (though the egg tastes like any boiled egg). More interesting are the various snacks (including baked yams) that you will find at the tourist places (not too touristy though).
The time is now ~ 3 pm and the question is whether you wish to press on down to the lake or head back to Gora and perhaps spend some moment wandering about. Recognize that most of the people traffic is heading down at this hour and there is often a long queue for the ropeway down to Togendai (lake).
If you press on to the lake, the final station is Togendai which is the boarding point for the pirate ship. Sadly on a single day visit it's not practical to take the boatride and it's now approaching 4 pm, best to wander about the lake side a while, grab a coffee and cake and at 5.30 reverse course head back as you came.
Note: Be mindful of the operation times as it varies during the year.
Important tip: It's not recommended to take the bus return from Togendai back to Hakone-yumoto. Yes there is a bus, however, the road return is quite hilly and slow and during the weekends crowded with vehicles and sadly not a great way to end your otherwise great day.