Why don't you make a one-day trip from Kyoto to Ninja's hometown Koka City?
Koka City is home of Ninja. Koka is a quiet, peaceful and beautiful rural town, and the best to go with a bicycle.
There is no tour to visit real Ninja places guided by a Ninja/local Samurai descendant who can speak English.
You can experience a very unique tour from this.

Tour starts from JR Konan station at 9:35am.
We will use electric bikes for transportation.

Koka Ninja House —It is the only existing real Ninja House with many tricks inside such as revolving door, hidden second floor, escape tunnel, too heavy sliding door, etc. You can throw Shuriken there if you want. Closed on Wednesdays.

Ninja Center —Local government built this Ninja Center for the Ninja's PR facility. There are many displays of Ninja weapons, clothes, papers, etc. Closed on Mondays.

Twin Castles —Hidden in the woods. These are listed as Nation's Historic Sites. Built more than 450 years ago.

Ninja-themed Restaurant —Many selection of dishes. There is a good Ninja's display room on the second floor.

Guide's house —The guide’s house is a typical Japanese house. We will make coffee by Ninja’s medicine making method. The guide's wife will write your name in Japanese katakana characters on Ninja’s roll paper for your sourvenir.

Ninja's sacred traing mountain, Mt. Iwao —Hiking to the top of the mountain. On the route, we will see the rock buddha statues, strange shaped huge rocks, beautiful lakes from the peak. Ninja used this mountain to do secret training.

Tour ends at JR Konan station.

(Optional) Ninja Village—In case Ninja House is closed, we will visit Ninja Village instead.

During this cycling tour, the guide will take some lovely photos of you.

On a rainy day, I have an alternative plan.

The itinerary can be customized according to your preference and time.