Central to the gameplay of Jidaigeki da yo Zenin Shūgō is the encounter map (accessed by pressing  and then  ). Finding these people results in either a boss battle or a cutscene. In order to progress the storyline you need to fight the bosses and watch the cutscenes, and the map will help you find your way.

Note that the map is not exact: a boss icon may be to the right of yours on the map, but this does not mean you actually go to the right of your current position to fight him. Bosses move about freely, so this walkthrough can only give the order in which they are fought. Some bosses are fought more than once during the course of the story. When you defeat a boss there is a chance that he will ask to join you. Simply pick a response and hit  (hitting  will decline the offer, regardless of which option the pointer is on). You can then change your partner in the starting house (where you met Bunzo).

One of the first items you should acquire is the Map CRSR (Map Cursor), which costs 3000 Ryo. This allows you to travel on the world map itself ( with  and  ) just as the other characters do.

The order of events is below. Optional events can be skipped, but all others cannot.

1. Game start
   • Ginpa (light blue) appears on the map
   • Gonsa (pink) appears on the map
2. Defeat the light blue gang and Ginpa
   • Ichi and Roku (yellow) appear on the map
   • Yono (grey) appears on the map
   • Cutscene with Sanki
3. Optional: defeat the pink gang and Gonsa
   • Gonsa might offer to join you
4. Defeat the yellow gang and Ichi & Roku
   • Heiru (green) appears on the map
   • Tame (dark yellow) appears on the map
   • Kinsu (blue) appears on the map
5. Optional: defeat Yono
   • Riki might offer to join you
6. Defeat the green gang and Heiru
   • Heiru (green) reappears
7. Defeat the green gang and Heiru again
   • Heiru might offer to join you
8. Defeat the dark yellow gang and Tame
   • Heisi (blue) appears
9. Defeat blue gang and Kinsu
   • Heisi (blue) appears (if you haven't beaten Tame yet)
10. Jinro (brownish yellow) appears after Heiru, Tame, Kinsu, and Heisi are all defeated
11. Defeat brownish-yellow gang and Jinro
    • Kinsu might offer to join you
    • Yono (grey) appears
    • Ginpa (light blue) reappears
    • Han (purple) appears
12. Optional: cutscene with Yono (you will receive Kanpou; take it back to Bunzo in Suruga and Bunzo will offer to join you)
13. Defeat purple gang and Han
    • Han might offer to join you
    • Gonsa might leave
    • Optional: Gonsa (pink) appears
    • Nizae (brown) appears
    • Yago (dark grey) appears
14. Optional: defeat dark grey gang and Yago
    • Juuki (grey) appears (only if Gonsa has been defeated)
15. Optional: cutscene with Juuki (he will offer to join you)
16. Defeat brown gang and Nizae
    • Tsui and Tatsu (dark blue) appear
17. Defeat Tsui and Tatsu (dark blue); one of them will run away
    • Heisi (blue) appears
    • Tsui or Tatsu (dark blue) reappears (whichever it was that ran away)
    • Tsui or Tatsu will offer to join you (whichever was beaten, as long as you didn't finish him off)
    • Cutscene with Okoto
18. Optional: cutscene with Heisi
19. Defeat dark blue gang and Tsui or Tatsu (whichever it was that ran away)
    • Tsuu leaves (if Juuki has joined), and appears on the map in dark green
    • Asaji (red) appears
20. Defeat red gang, watch Asaji cutscene
    • Heisi (blue) appears.
21. Second cutscene with Heisi (blue)
    • Kinsu may leave
    • Tora (black) appears
22. Optional: defeat dark green gang and Tsuu (Tsuu may rejoin)
23. Defeat black gang and Tora
    • Juuki may join, or leave if he's already joined
    • Kinsu may rejoin
    • Yago (dark grey) appears
    • Asaji (red) reappears
24. Optional: defeat grey gang, watch cutscene with Yago (receive Goodtime Charm)
25. Defeat red gang and Asaji (along with Juuki, if he left)
26. Return to Bunzo's place in Suruga to watch the ending

The hungry man will appear and say, "Dum-de-dum... doesn't this story grab you? You finished it? Don't you have a life? Maybe we'll meet again... and kick your ass! The end!" It's not quite the end yet, though. After this you get offered Okoto's hand in marriage. If you decline Kunio will leave, explaining that he is a drifter and that she deserves better. If you agree, Kunio gets the girl... and some sake!