I'm confused on buying train tickets

I'm doing some research. We are trying to travel from Tokyo to Habuka. There is a direct train. Can I book just this train? Also, on the way home we want to book a bus and a bullet train by to Tokyo. Can we book these seperate?? Please help. Thank you!!

Can I book just this train?

Yes, of course.

Also, on the way home we want to book a bus and a bullet train by to Tokyo. Can we book these seperate?

You have to, because the train and bus are operated by separate companies and won't sell eacj other's tickets.

We are trying to travel from Tokyo to Habuka. There is a direct train. Can I book just this train?

I don't think there is any direct trains from Tokyo Station to Hakuba Station (correct me if I'm wrong). Are you perhaps talking about the Azusa 5 express departing Shinjuku Station at 8 am going directly to Hakuba Station? If so, yes, you can book just the Azusa 5 train.

But depending on how you buy the tickets, you could be missing your chance to save money. Maybe that's what you're confused about.

JR express trains (such as the Azusa express and the bullet trains) consist of (A) the basic fare ticket and (B) the express surcharge ticket. The express surcharge ticket is always just for that specific express train. On the other hand, the basic fare ticket is a "through ticket" that covers your whole trip on JR company trains.

Let's say you're traveling from Shibuya to Hakuba. A basic fare ticket from Shibuya to Hakuba via Shinjuku is 5500 yen, which is the same as the basic fare ticket from Shinjuku to Hakuba is 5500 yen. Adding the express surcharge of 2550 yen, the total price you'd be paying one way would be 8050 yen.

But a ticket from Shibuya to Shinjuku is 170 yen. So, if you buy a ticket from Shibuya to Shinjuku, and a ticket from Shinjuku to Hakuba separately, it would add up to 8220 yen instead of 8050 yen.

So, if you're booking express trains, be sure to buy only the express fare ticket. You can buy the basic fare ticket after you've decided where you're really departing from.

Or if you've already decided the first station you're boarding a train, let us know and perhaps someone could help you.