Chapter Challenge mode - Successfully complete the game to unlock Chapter Challenge mode.

Master Ninja mode - Successfully complete the game on the Mentor difficulty to unlock the Master Ninja difficulty.

Mentor mode - Successfully complete the game on the Acolyte or Warrior difficulty to unlock the Mentor difficulty.

Team Mission mode - Successfully complete the first mission in Story mode to unlock Team Mission mode.

Gold health bar - Successfully complete the game on the Master Ninja difficulty to have a golden health bar.

Music test - Successfully complete the game to unlock the "Music Test" option at the options menu.

Alternate costumes - Successfully complete the indicated task to unlock the corresponding costume:

Ayane's Dynasty Warriors (Son Shokou) costume: Successfully complete 20 missions in Team Mission mode.
Ayane's Sigma 1 (hooded) costume: Successfully complete the game on the Acolyte or Warrior difficulty.
Momiji's Dragon Sword (training) costume: Successfully complete the game on the Acolyte or Warrior difficulty.
Momiji's Dynasty Warriors (Sanzo Houshi) costume: Get the "Master Ninja" rank on 30 Chapter Challenges.
Rachel's Assassin Rachel (short hair) costume: Successfully complete the game on the Acolyte or Warrior difficulty.
Rachel's Cutie Rachel (long hair) costume: Successfully complete the game on the Acolyte or Warrior difficulty.
Rachel's Dynasty Warriors (chosen) costume: Successfully complete the game on the Mentor difficulty.
Rachel's Sweet Rachel (curly hair) costume: Successfully complete the game on the Acolyte or Warrior difficulty.
Ryu's Classic Hayabusa (Ryuken) costume: Successfully complete 10 missions in Team Mission mode.
Ryu's Devil Hayabusa (Fiend) costume: Successfully complete the game on the Acolyte or Warrior difficulty.
Ryu's Dragon Clone Hayabusa (Ninja Gaiden Sigma) costume: Get the "Master Ninja" rank on 10 Chapter Challenges.
Ryu's Dynasty Warriors Hayabusa (Choun Shiryu) costume: Successfully complete the game on the Mentor difficulty.

Jiggle Rachel's chest - Shake a Sixaxis controller to make Rachel's chest jiggle.

Trophies - Successfully complete one of the following tasks to get a trophy:

Learned the Reverse Wind (Bronze): Successfully perform the Reverse Wind technique.
Learned the Furious Wind (Bronze): Successfully perform the Furious Wind technique.
Learned the Shadowless Footsteps (Bronze): Successfully perform the Shadowless Footsteps technique.
Learned the Flying Swallow (Bronze): Successfully perform the Flying Swallow technique.
Learned the Flying Bird Flip (Bronze): Successfully perform the Flying Bird Flip technique.
Learned the Obliteration Technique (Bronze): Successfully perform the Obliteration Technique.
Learned the Ultimate Technique (Bronze): Successfully perform the Ultimate Technique.
Learned the Ultimate Guidance (Bronze): Successfully perform the Ultimate Guidance technique
Learned to the Counter Attack (Bronze): Successfully perform the Counter Attack technique.
Learned the Unrivaled Soaring (Bronze): Successfully perform the Unrivaled Soaring technique.
Learned the Invisible Path (Bronze): Successfully perform the Invisible Path technique.
Learned the Izuna Drop (Bronze): Successfully perform the Izuna Drop technique.
Learned the Guillotine Throw (Bronze): Successfully perform the Guillotine Throw technique.
Learned the Art of the Inferno (Bronze): Successfully perform the Art of the Inferno Ninpo.
Learned the Art of the Wind Blades (Bronze): Successfully perform the Art of the Wind Blades Ninpo.
Learned the Art of the Flame Phoenix (Bronze): Successfully perform the Art of the Flame Phoenix Ninpo.
Learned the Art of the Piercing Void (Bronze): Successfully perform the Art of the Piercing Void Ninpo.
Feat of a Hundred Slashes (Bronze): Achieve a 100-hit combo with any weapon.
Feat of a Thousand Obliterations (Bronze): Defeat 1000 enemies unsing Obliteration Techniques.
Feat of Ultimate Destruction (Bronze): Defeat 1000 enemies using Ultimate Techniques.
Izuna Drop Master (Bronze): Successfully use the Izuna Drop on 1000 enemies.
Guillotine Throw Master (Bronze): Successfully use the Guillotine Throw on 1000 enemies.
Dragon Sword Master (Bronze): Defeat 1000 enemies with the Dragon Sword.
Lunar Staff Master (Bronze): Defeat 1000 enemies with the Lunar Staff.
Falcon's Talons Master (Bronze): Defeat 1000 enemies with the Falcon's Talons.
Dual Katana (Bronze): Defeat 1000 enemies with the Dual Katana.
Kusari-gama master (Bronze): Defeat 1000 enemies with the Kusari-gama.
Eclipse Scythe Master (Bronze): Defeat 1000 enemies with the Eclipse Scythe.
Tonfa Master (Bronze): Defeat 1000 enemies with the Tonfa.
Vigoorian Flail Master (Bronze): Defeat 1000 enemies with the Vigoorian Flail.
Enma's Fang Master (Bronze): Defeat 1000 enemies with the Enma's Fang.
Ultimate Ninpo Master (Bronze): Chant 100 Ultimate Ninpo spells.
Rescued 100 ninja (Bronze): Rescue 100 people in need.
All missions successfully completed (Gold): Successfully complete all missions.
Master of the Secret Arts (Platinum): Obtain all trophies.

Additionally, there are sixteen secret trophies:

Completed Chapter 1 (Bronze): Successfully complete Chapter 1.
Completed Chapter 2 (Bronze): Successfully complete Chapter 2.
Completed Chapter 3 (Bronze): Successfully complete Chapter 3.
Completed Chapter 4 (Bronze): Successfully complete Chapter 4.
Completed Chapter 5 (Bronze): Successfully complete Chapter 5.
Completed Chapter 6 (Bronze): Successfully complete Chapter 6.
Completed Chapter 7 (Bronze): Successfully complete Chapter 7.
Completed Chapter 8 (Bronze): Successfully complete Chapter 8.
Completed Chapter 9 (Bronze): Successfully complete Chapter 9.
Completed Chapter 10 (Bronze): Successfully complete Chapter 10.
Completed Chapter 11 (Bronze): Successfully complete Chapter 11.
Completed Chapter 12 (Bronze): Successfully complete Chapter 12.
Completed Chapter 13 (Bronze): Successfully complete Chapter 13.
Cleared the Path Of The Warrior (Silver): Clear the game on the Path Of The Warrior.
Cleared the Path Of The Acolyte (Silver): Clear the game on the Path Of The Acolyte.
Secret trophy (Unknown): Unknown.