which rail way ticket should i buy?

i am going on a 12 days trip to japan. covering tokyo, nikko, kamakura, hakone, fuji five lake(kawaguchiko), kyoto and hokkaido. i cant find a rail way transport that covers all the stations. please advice me. thanks

If you have only 12 days, you will have to fly to Hokkaido in order to pack all these destinations in. And you will have only two days or so in Hokkaido.

Which airports are you able to use to enter and leave Japan?

If you can enter Japan through Hokkaido (Sapporo Airport has direct flights to some Asian destinations), the following route would be very efficient:

Enter Japan through Sapporo, visit Sapporo, fly to Tokyo, see Tokyo with side trips to Nikko, Kamakura, Hakone and Fujigoko, then take the shinkansen to Kyoto and leave Japan through nearby Kansai Airport.

If you cannot enter Japan through Hokkaido, the following would be an efficient route:

enter through Tokyo's Narita Airport - Tokyo - (fly) - Hokkaido - (fly) - Kyoto - leave through Osaka's Kansai Airport

For the flights, I recommend to use an air pass, if possible. More details:
http://www.japan-guide.com/e/e2364.html

air ticket is very expensive.is there any train pass that i can buy that go to tokyo,nikko,kamakura,hakone, fuji five lake, kyoto and osaka? which train route should i take???

12 days is jammed packed if you want to save money then knock out Hokkaido from your trip (just my opinion), if you need to save money then taking a overnight bus between some of the places like Tokyo-Kyoto would be cheaper. If you must go to Hokkaido it is cheaper and faster to fly in my opinion with a discount air ticket.

Places like Kawaguchiko is definitely better accessed by bus then train.

There is no one railpass that covers your entire route.

Rachel, I do hope you haven't pre booked hotels yet. Get a 7 day JR pass. Do Tokyo to Kyoto and back in that period. Try very hard to include Nikko in the period of the pass so that you can get there by shinkansen (part of the way at least ). I asume you are flying in to Narita; if so kick the pass off immediately and go straight to Kyoto ASAP. If you can fit Kamakura in it will save you a few pennies but it isn't too important $$$ wise. For Hakone you can use JR or Odakyu Rwy and there are combination tickets to save you some money. 12 day trip.....absolutely forget Hokkaido unless you are going for the snow festival in which case you would have to fly. Even using a night train you would lose a day each way.
My choice of train planning is http://www.hyperdia.com/cgi-english/hyperWeb.cgi
And no you will not find stations everywhere. Fuji/Hakone must be done by buses in places where there are no trains. It is all covered on some combination tickets....search this site some more.

so can i just buy the tickets one by one? like from tokyo to kyoto. then kyoto to the places. by the way. where can i take the bus to fuji and hakone?

so can i just buy the tickets one by one? like from tokyo to kyoto. then kyoto to the places. by the way. where can i take the bus to fuji and hakone?

can you all recommand me what rail pass should i buy??