Here's the general idea. You are dealing with two days only in the life of this little pass. There are two clans vying for power - the Kuroa clan, headed by Tesshin, and the Akadama clan, headed by Tesshin's son, Kitcho. The Kuroas want to sell a foundry to the government and evict the townspeople. The Akadamas hate the government and want to stop this sale. The townspeople are caught in the middle of this.

There are four time periods. Daytime on Day 1, Evening on Day 1, Nighttime on Day 1, and Daytime on Day 2. That's it. Certain things happen in each time period, and either you're there to see them happen, or you're not. Some of the important things are:

Day 1 Daytime
Suzu is kidnapped by Kuroa clan and rescued
Kyuga meets with the government people at the shrine
You can duel Shiretoko if you want to join the Kuroa
The Kuroa go to roust Suzu from town

Day 1 Evening
The Akadama plot in their castle at a table
The Kuroa walk their baby, the Akadama attack it
Dona writes love poetry on the bridge

Day 1 Night
Suzu worries where Dona is
Dona is at the Kuroa residence, stealing a chest
Various troops are attacking each other on the roads
Murasaki has an affair with the policeman at the shrine

Day 2 Daytime
The final conflict occurs (depending on who is still alive and is angry at who)

Way of the Samurai Walkthrough