Unlockable Missions and Story:
S Rank Missions - Complete the game once.
Kakashi Gaiden (Story) - Complete all missions (including S Rank Missions)
Unlockable Characters in "Two Player Vs." mode:
Sasuke - Complete "Story" mode two times.
Hoshigake Kisame - Complete Kakashi Gaiden story.
Uchiha Itachi - Complete Kakashi Gaiden story.
During loading screens that have an icon of Konoha in the lower right-hand corner, rotate the right analog stick until a blue Chakra ball appears. Doing so will refill a small amount of your character's Chakra.