Protagonist
- N.Y.N.'s Leader - Keith Kyle Dakins a.k.a. Red Ninja or Kaen (Ninja of Flame)
- N.Y.N.'s 2nd in Command - Kito Sugiwari a.k.a. Blue Ninja (Ninja of the Ocean)
- N.Y.N.'s 3rd Member - Hachi Mora a.k.a. Purple Ninja (Time Ninja/of Time)
- N.Y.N.'s 4th Member - Tsugi Mora a.k.a. Orange Ninja (Thunderstorms Ninja/of Thunderstorms)
Support/Minor Characters
Friends and Family
- N.Y.N.'s 5th Member and Nate's Older Sister (Onēsan) - Nexus Kumori
- N.Y.N.'s 6th Member - Sugimori
- N.Y.N.'s 7th Member and Keith's Girlfriend - Tristana "Trista" Anderson
- N.Y.N.'s 8th Member - Mär Rēdō
- Kōtori-Sensei - Traditional Martial Arts and Secret Ninja Teacher
- Ādō Watashii - Hidden Ninja Clan's Teacher
- Sawagi - Traditional Martial Arts Substitute Teacher
- Princess Hana Yumeno
- Nate Kumori - Nexus's Little Brother (Otōto)
- Drake Dakins - Keith's father
- Setsuna Dakins - Keith's mother
- Sunamori - School Math Teacher
- Chōkaro Kibo - Kyle's School Friend
- Shara Tonami - Trista's School Friend
Hidden Ninja Clan a.k.a. The Rune Clan
- Member 1 - Tiger's Eye a.k.a. Tora Meno*<
- Member 2 - Shark's Teeth a.k.a. Same Hano
- Member 3 - Wolf's Fang a.k.a. Ookami Kibano
- Member 4 - Shadow Snake a.k.a. Hebi Kageno*<
- Member 5 - Panda's Claws a.k.a. Kumaneko Tsumeno
- Member 6 - Dragon's Force a.k.a. Ryū Chikarano<
- Member 7 - Monkey's Strike a.k.a. Saru HashiMukaino*<
- Member 8 - Fox's Tail a.k.a. Kitsune Ono
- Member 9 - Rabbit's Speed a.k.a. Usagi Hayano<
- Member 10 - Tortoise's Bite a.k.a. Kame Kamuno
- Member 11 - Crane's Balance a.k.a. Tsuru Shūshino*
- Member 12 - Mantis's Stancea.k.a. Tōrō Kangaekatano*
- Member 13 - Lion's Whiskers a.k.a. Shishi Higeno
- Member 14 - Dog's Howling a.k.a. Inu Toboeno<
- Member 15 - Princess Panda's Claws a.k.a. Kumaneko-Hime Tsumeno
*= Kung Fu battle styles
<= Chinese Zodiac Ninjas
The Missing Chinese Zodiac Ninjas
- Member 16 - Rat's Ears a.k.a. Nezumi Mimino
- Member 17 - Ox's Horns a.k.a. Ushi Tsunono
- Member 18 - Horse's Stamina a.k.a. Uma Sutaminano
- Member 19 - Sheep's Hooves a.k.a. Hitsuji Hidzumeno
- Member 20 - Rooster's Talons a.k.a. Rūsutā Taronno
- Member 21 - Boar's Tusk (or Ivory) a.k.a. Inoshishi Zōgeno (Yězhū de liáo yá)
Antagonist
- Kuro Sedo Kuno a.k.a. Illusion X
- Dark X or Kurai X
Places
- New York City, USA
- Tokyo, Japan
