Ayame and Rin both have unlockable weapons which when unlocked and the Chapter completed will always be available at your 'Item' selection.

Unlock Ayame's Dokuto Blades Weapon:
In Chapter 7.1 or 7.2 of Story mode reach the room across from the Boss battle room. (if you use the shortcut this room will be sealed).

Unlock Ayame's Fake Rat:
In 'Level Select' mode complete Chapter 10-1 or 10-2 with a 'Grandmaster' rank.

Unlock Ayame's Sleeping Gas:
In 'Level Select' mode complete Chapter 12-1 or 12-2 with a 'Grandmaster' rank.

Unlock Rin's Decoy Whistle:
In 'Level Select' mode complete Chapter 11 with an 'Assassin' rank.

Unlock Rin's Demon Claws Weapon:
In Chapter 8 of Story mode cross the bridge and move left along the wall. Then double jump over to the little ledge.

Unlock Rin's Fire Spell:
In 'Level Select' mode complete Chapter 9 with an 'Assassin' rank.

Unlock Ayame's Alternate Costume:
Collect 1,600 scrolls to unlock Ayame's original costume from 'Tenchu: Stealth Assassins' and 'Tenchu 2: Birth of the Assassins'.

Unlock Rin's Alternate Costume:
Complete the game to unlock Rin's alternate costume and Ayame's original costume from 'Tenchu 3: Wrath of Heaven'.

Red Blade Mode:
Obtain a Grandmaster or Master of Assassins Ranking in all 18 levels

Ninja Rebirth Item:
Complete Training Stage

Sound Check Mode:
Beat every layout on every skill level with each character

Pit Fight Mode:
Beat the game on Normal difficulty

Pit Fight Mode Boss Fights:
Defeat all 6 enemy groups in Pit Fight mode.


Missions
Play Story mode to unlock the missions

Chapter 2.1 - Departures:
Do not Eliminate all enemies in mission 1

Chapter 2.2 - Determination kill:
Eliminate all enemies in mission 1

Chapter 6.1 - The Blind Masseuse:
At least one enemy spot you in mission 5

Chapter 6.2 - What Lurks in the shadow:
You must not be spotted in mission 5

Chapter 7.1 - A Sister's Promise:
Get the map in mission 6

Chapter 7.2 - For Whom the Bell Tolls:
Don't Pick up the map in mission 6

Chapter 10.1 - Flames of Passion:
Don't eliminate the Samurai at the beginning of mission 9

Chapter 10.2 - Flames of Sorrow:
Eliminate all 3 enemies at the beginning of mission 9

Chapter 12.1 - Tenchu Kurenai:
Eliminate Ranzo

Chapter 12.2 - Tenchu Kurenai:
Let Ranzo escape


Unlockable Special Abilities
Unlock the following by obtaining the corresponding number of scrolls in Story mode.

Wall Run Ayame:
10 Scrolls / Rin: 100 Scrolls

Hawk Eye Ayame:
60 Scrolls / Rin:150 Scrolls

Arrow Block Ayame:
250 Scrolls / Rin:30 Scrolls

Long Claw Ayame:
300 Scrolls / Rin: 350 Scrolls

Sniper Ayame:
350 Scrolls / Rin: 450 Scrolls

Spider's Nest Ayame:
450 Scrolls / Rin: 400 Scrolls

Crescent Moon Ayame:
30 Scrolls

Swift Guard Ayame:
100 Scrolls

Cheetah Sprint Ayame:
150 Scrolls

Inner Ear Ayame:
200 Scrolls

Mind Control Ayame:
400 Scrolls

False Wall Ayame:
500 Scrolls

Wrath Ayame:
550 Scrolls

Fang Guard Rin:
10 Scrolls

Death Drop Rin:
60 Scrolls

Crimson Rin:
200 Scrolls

Numbing Strike Rin:
250 Scrolls

Shadow Rin:
300 Scrolls

Mimicry Rin:
500 Scrolls

Crimson Final Rin:
550 Scrolls