Neither version was released outside of Japan.
- Goemon: The main protagonist and titular character of this spin-off series series.
- Ebisu: She's the best friend of the Goemon from the future. She wields the same weapons as Ebisumaru and is possibly his daughter.
- Sasuke (Mark 2): A clockwork robot ninja. He wields the same weapons as Sasuke.
- Yui: An equivalent of Yae, and as such, wields the same weapons.
- Hanzō: The boss of the first stage: Haikyo.
- Kojirō: The boss of the second stage: Yami.
- Benkei: The boss of the third stage: Chugi.
- Musashi: The boss of the fifth stage: Oni, before the main boss: Yoshitsune's Black Impact.
- Yoshitsune: One of the main antagonists. He is first encountered as the boss of the fourth stage: Mato, and later as the boss of the fifth stage: Oni, this time while piloting Black Impact.
- Kiyohime: One of the main antagonists and final boss of the game.
- Area 1: Haikyo - Bosses: Hanzō, Hide Impact
- Area 2: Yami - Boss: Kojirō
- Area 3: Chugi - Bosses: Benkei, Heavy Impact
- Area 4: Mato - Boss: Yoshitsune
- Area 5: Oni - Bosses: Musashi, Black Impact
- Area 6: Naraku - Final boss: Kiyohime