The missions will all be created with Shinobi Taizen's map construction mode, which lets users make their own missions. Gamers can share their own original missions via a Memory Stick Duo or the Internet, which is how the special stages will also be offered.

Unlockables
Onikage story mode:
Successfully complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Illusion special mission:
Successfully complete Onikage story mode.

Tenchu special mission:
Successfully complete the Illusion special mission.

Play as Bear:
Complete Onikage's story mode.

Play as Echigoya:
Complete the Tenchu special mission .

Play as Jinnai:
Complete Tesshu's story mode.

Play as Jonosuke:
Complete Ayame's story mode.

Play as Juzo:
Complete Rin's story mode.

Play as Kenpo Bozo:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Kunoichi:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Kuroya Jo-Kunoichi:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Kuroya Jonin:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as merchant:
Complete the Tenchu special mission.

Play as Mifuyu:
Complete Ayame's story mode.

Play as monk:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Mr. D:
Complete the Illusion special mission.

Play as ninja:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Ninja dog:
Complete Onikage story mode.

Play as Onikage:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as policeman:
Complete the Illusion special mission.

Play as Ranzo:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Ronin:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as salary-man samurai:
Complete the Illusion special mission.

Play as Samurai:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Shimatsuya doctor:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Shimatsuya female:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Shimatsuya samurai:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Shimatsuya villager:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Shinogi:
Complete Tesshu's story mode.

Play as Sho:
Complete Rikimaru's, Ayame's, Rin's and Tesshu's story modes.

Play as Tajima Eigoro:
Complete Rin's story mode.

Play as Tatsumaru:
Complete Rikimaru's story mode.