Las misiones son encargos que se dividen en distintos rangos según la dificultad. Por realizarlas te recompensarán con dinero (Ryo), algunas veces objetos, o desbloquear nuevas misiones.
Al empezar debes seleccionar una misión y tras una breve descripción de ella, y luego de aceptarla, podrás seleccionar cual o cuales personajes utilizar en ella. Las misiones son 46 en total:
9 Rango D 13 Rango C 12 Rango B 7 Rango A 5 Rango S
Misión - Objeto de premio - Ryo
Rango D:
No mercy for evil! - Nada - 50 Destroy the goods! - Nada - 50 Crush the rouge ninja - Medicine C - 70 Losers Weepers! - Rations C - 110 I've got your back, Choji! - Nada - 100 Strength in number - Medicine C - 130 Where's Sakura? - Nada - 110 You want spies with that? - Rations C - 130 The mountain bandit's forest! - Medicine C - 220
Rango C:
The masked mob - Nada - 60 The bandits strike back - Nada - 100 Treasure watcher - Medicine C - 110 Expiration date? - Medicine C - 120 Crime doesn't pay! - Nada - 160 Mysterious machines - Nada - 150 To catch a outlaw- Nada - 200 The kunoichi caper - Medicine B - 250 Choji under attack! - Medicine C - 220 Bridging the gap - Medicine C - 240 Dirty traders - Medicine B - 300 Revenge of the blade - Medicine A - 320 Monkeys at large - Medicine X - 350
Rango B:
Crime still doesn't pay! - Revive C - 170 Bad bandits! No supper! - Medicine B - 250 The unkindest cut - Rations C - 230 Danger! Monkey menace! - Medicine B - 270 To the land of Wind! - Revive B - 270 Ticket collector - Revive C - 320 Hot pursuit - Medicine B - 450 Get the flowers! - Rations A - 450 No more monkeying around! - Dual C - 420 Know your enemy! - Revive A - 600 Lights out! - Dual A - 550 Wild puppets! - Dual X - 550
Rango A:
Handle with care - Rations B - 320 Bridge patrol - Rations B - 350 Gathering intelligence - Rations A - 370 Secret against escort - Medicine B - 380 Lord of the
Monkeys!? - Rations X - 400 Sakura SOS! - Dual A - 400 Destroy the puppetmaster! - Rations X - 600
Rango S:
Puppet crisis - Medicine X - 1000 Playing with fire - Rations X - 1500 The Shirogane's shadow - Rations X - 1200 The fires of vengeance - Revive A - 1000 Protect the checkpoint - Dual X - 1200