To gain access to the full tutorial with Ayame you must hold L1 while selecting the Tutorial. No onscreen confirmation will be given but once the tutorial starts you will be using Ayame instead of Rin.
Ayame Chapter 7.2: Dokuto Blades
In the room across from the Boss Battle room provided you did not take the shortcut.
Ayame's Tenchu 1 and Tenchu 2 costumes
Defeat Juzo in Pit Fight mode with more than 23 minutes remaining and defeat the two Ayames. Alternatively, collect a total of 1600 scrolls.
Chapter 3: Tatsukichi instant kill
Run up to this boss, push towards them, and hit circle to perform a throw. Both Ayame and Rin will administer not their normal throw, but a neck chop that instant kills this boss.
Cutscenes with armor on
When viewing already unlocked cutscenes in the Encyclopedia section, press and hold L2 while selecting a cutscene and when it loads you will get to see Ayame or Rin wearing their Armor during it.
Level Select Mode: Third Enemy Layout
Complete all the playable missions in Story mode.
Missions
Effect - Code
2.1 Departures - Do not eliminate all enemies in mission 1
2.2 Determinationkill - Eliminate all enemies in mission 1
6.1 The Blind Masseuse - At least one enemy spot you in mission 5
6.2 What Lurks in the shadow - You may not be spotted in mission 5
7.1 A Sister's Promise - Pick up the map in mission 6
7.2 For Whom the Bell Tolls - Do not pick up the map in mission 6
10.1 Flames of Passion - Do not eliminate the samurai at the beginning of mission 9
10.2 Flames of Sorrow - Eliminate all 3 enemies at the beginning of mission 9
12.1 Tenchu Kurenai - Eliminate Ranzo
12.2 Tenchu Kurenai - Let Ranzo escape
Note: You must play story mode to unlock the missions.
Pit Fight Mode
Successfully complete the game under the normal difficulty setting.
Pit Fight mode Boss Fights
Defeat all 6 enemy groups in Pit Fight mode.
Rin Chapter 8: Demon Claws
After crossing the bridge head left along the wall and double jump over to the little outcropping ledge.
Rin's hidden costume, Ayame's Tenchu 3 costume
Beat the game on any difficulty.
Unlock Ninja Rebirth Item
Complete Training Stage.
Unlock Red Blade Mode
Get a Grandmaster or Master of Assassins Ranking in all 18 levels.
Unlock Sound Check Mode
Beat every layout on every skill level with each character.