Best use of a short rainy visit: stay in the UNESCO shrine/temple zone, then finish with a proper natural onsen if you have time. Skip Lake Chuzenji and Kegon Falls for this short window.
Station → World Heritage bus or ~25–30 min uphill walk. Once at Shinkyo, everything else is close on foot.
Take the World Heritage sightseeing bus from the station if rain is steady. Walking is fine only if you want the exercise.
Quick photo stop. Rain and mist actually make the red bridge and forest look excellent.
Good rainy-day indoor stop.

Main event. Spend most of your time here: Yomeimon Gate, famous carvings, inner shrine if you feel like stairs in the rain.

Quieter and more atmospheric than Toshogu, especially in wet forest conditions.
If 2 hours total: head back after Toshogu. If 3 hours: add Futarasan. If 4 hours: add an onsen below before returning to JR Nikko.
Near Shinkyo. Traditional ryokan with natural hot-spring baths and a garden view. Very convenient after Toshogu compared with going out to Kinugawa or Yumoto.

Directly by JR Nikko Station. Natural hot spring with indoor and open-air baths, so it works well as the final stop before leaving Nikko.

Tokorono; taxi is easiest. Small natural hot-spring facility with open-air bathing.
