Among the different side missions you can complete in Onimusha: Way of the Sword are the Mysteries of Kyoto. These are a series of requests from Lady Murasaki that will have you investigate strange events throughout the city.
This Mystery is activated automatically at the end of What Lurks in the Shadows and must be completed to progress. The marker appears at Kiyomizu-zaka Slope.
Speak to the boy to find out what's wrong. You'll be sent to the southeast of Kiyomizu-dera, to the checkpoint you passed through near the beginning of the game. A cutscene will play as you approach the area. The marker will then move to the central area, where you'll encounter the man again. Genma and a Rift will appear, and you'll need to seal it. The mission will be completed afterwards.
This mission appears once you reach The Roots of All Evil. The marker is in the southeastern part of Eastern Kyoto, very close to where the previous Mystery began, around Kiyomizu-zaka Slope.
Speak to the man in the street to hear what he has to say. The marker will move east of Rokudo-chinnoji Temple, so head there. After the cutscene, follow him to Nenbutsu Temple; the marker will guide you to this location east of the Kamo River. After another cutscene, defeat the Genma and the Malice-emitting plant, then head to the new marker in the northwestern corner of the region. You can enter the compound by heading to the northern edge and taking the gate on your left.
Defeat one final group of Genma to complete the mission.
This mission becomes available when you begin Shadows Fall. You'll find the marker in southeastern Kyoto, near the Kiyomizu-zaka Slope Spirit Mirror.
Enter the marked house and speak to the coughing man. The marker will take you to Nio-mon Gate at Kiyomizu-dera. Climb the stairs to find a woman who knows who you're looking for. The marker will then move east-southeast to the Temple Grounds. Approach the balcony to speak to a couple, and you'll then be sent to a building to the east. Go around the corner of the temple to find the woman standing in front of a small shrine, triggering a cutscene.
You'll then need to head north to seal a Rift. Only regular Genma will appear. Once you've sealed it, return to the woman. The mission ends after the cutscene.
This mission becomes available when you begin To Live is to Suffer. You'll find the marker in southeastern Kyoto, near the Kiyomizu-zaka Slope Spirit Mirror. You must have completed the previous Mystery for it to appear.
Enter the house to trigger a cutscene. You'll be sent to Kiyomizu-dera, southeast of the Temple Grounds, south of where the previous Mystery ended. Speak to the woman beside the pond to continue. You'll then be sent to the altar where the wife from the previous mission was praying, up the stairs and to the east. A barrier maintained by two Weavers will appear: one is on the rooftop to the north, fairly close by, while the other is in the lower area, farther downstream.
Return to Yashajin Hall so Murasaki can explain that there are more problems. Head down to the waterfall, defeat the Genma and then examine the pond. The mission will be completed afterwards.
This mission becomes available when you begin The Demon on the Mount. You'll find the marker north of Rokudo-chinnoji Temple, beside Yorimasa's altar. Speak to the blind woman you met earlier to begin the mission.
You'll be sent to the southeastern part of Kyoto's northwestern district. To enter the compound, look for the ladder in the southwestern corner of the complex.
Once you climb up, you'll see that you can slip through an open window into an inner courtyard. The courtyard door won't open unless this mission is active, but it will now. Follow the only available route, defeat the enemies and open a chest containing Cotton Cloth x2. At the end, destroy a Malice Barrier and open the door to the next building to trigger a cutscene. Afterwards, you'll need to defeat some Genma. The mission ends after the battle.
This mission becomes available when you begin The Demon on the Mount. The marker appears east of Rokudo-chinnoji Temple. Speak to the strange woman to find out what's going on.
Once you reach the search area, approach the house shown below. A cutscene will play and you'll need to defeat a Genma.
After the battle, find the second hall in a courtyard in the northeastern part of the search area. Follow the route shown below to enter through a gap in the fence.
Defeat another couple of Genma and head directly to the final search area. This one is smaller and will point you directly to where you need to go, where you'll find a monk to speak with. Defeat one final group of Genma to complete the mission.
This mission becomes available starting from A Haunted Distraction. The marker appears in the northern part of the sandbar, in the northwestern corner of Kyoto.
The marker will take you southwest of Yasaka Shrine, in northeastern Kyoto. Sure enough, among the market stalls you'll find the parade: a group of Genma. Defeat them, then head to the riverbank in the second search area to find more Genma. The third parade circles around north of the marker in the center of the search area, through the fields. It's a large group led by a Byakue. The mission ends once you've defeated them.
This mission becomes available starting from A Haunted Distraction. The marker appears east of Rokudo-chinnoji Temple.
You'll be sent to... a place you visited a long time ago. Climb the stairs to trigger a cutscene. All you need to do is defeat three regular enemies.
