Hi Robin, there are multiple options – however JR does not control the local lines in Hakone. But once you reach Odawara, you may use your JR Pass.

There is a great tool for routes and timetables called Navitime, you can read more about it here: https://getjrpass.com/tools/

I’m not sure exactly where you are located in Hakone, but using Hakone-Yumoto as a starting example, you may take the Hakonetozan Railway Local(Odawara-HakoneYumoto) to Odawara (not included in the JR Pass but only costs 2 USD/EUR). From Odawara, take the Hikari Shinkansen for 33 minutes to Tokyo  which is included in the JR Pass 😊