In the Edo period in Japan, there was a shadowy group of vigilante ninjas - they did anything, even murder, as long as they got paid.
One day, the well-respected police constable Takao and his wife were accused of a crime and murdered. They were the parents of a teenage girl named Yui, the Player Character of the game, who survived thanks to her mother's quick intervention; filled with sadness and anger, Yui made up her mind to avenge the deaths of her parents, and then she remembered there were assassins known as the vigilantes. Soon after that, she tried to get in touch with them, but she didnt get any replies.
As she was about to give up, one of the vigilantes appeared in front of her and took to a tea house. After listening to her story, he suggested her join them to take vengeance on the people who murdered her parents. After a moments thought, she decided to take up his suggestion.
Alongside the vigilante ninjas, she started her pursuit of justice.
Shall We Date?: Ninja Assassin provides examples of:
- Agent Peacock: Aoi and Hotaka are very girly-looking guys, plus very good fighters as well.
- Big Bad: Lord Yozo Tori, the man who ordered the deaths of the Takaos for supposedly being involved in illegal activities. Yui survived because her mother managed to hide her under the floor board, and now she wants revenge.
- Big Brother Mentor: Some of the Vigilantes take up this role to the Naïve Newcomer Yui, especially Kinshiro.
- Childhood Friend Romance: It turns out that Ichika, Soujis co-worker, is a long-time friend of Yui. This will happen if he's the chosen boyfriend.
- Corrupt Corporate Executive: Willem, a Dutch tycoon involved in many legal and illegal activities. And he's a potential boyfriend for Yui.
- Dark and Troubled Past: Some characters have suffered a lot in their pasts:
- Hotaka lost his parents very early in his life, due to an illness. He was taken in by Sion's family.
- Wakasa is the Sole Survivor of a whole ninja village, and he saved his own life by killing almost everyone in the group that raided it. That's the original of his Blood Knight side that arises in battle, and he's deeply troubled over it.
- Willem was the son of a rich Dutch merchant family, who were murdered by their business rivals. After being homeless and destitute, he was tricked into joining an assassin group named Red Roses and eventually became a Corrupt Corporate Executive.
- Defrosting Ice King: Soji becomes this in his own route. His initial behavior towards Yui is apathetic at best, but after she expresses gratitude for him being honest with her, he starts acting more openly compassionate and even Adorkable at times.
- Tsundere: male example Natsume
- Fair Cop: Soji and Ichika are police constables in their day job.
- Faceless Protagonist: Averted with Yui, whose face can be clearly seen in several CG's.
- Frame-Up: A fatal one targeted Yui's parents.
- He Knows Too Much:
- Yui speculates that this is the real reason why her father was framed: being a constable, he probably found out about any prospect illegal business done by Tori, and he killed the Takaos to save his own ass. In at least one route, she directly confronts Tori and he confirms her theory.
- When Yui was about to contact the Vigilantes, she witnessed one of their killings. Since she was going to ask them for help, Kinshiro told her that either he'd kill her for seeing what she shouldn't, or she'd have to join the group.
- In Aoi's route, a person he knows gets killed off for this reason. His friend Chidori was The Mistress of Tori's henchman Satake and found out about his illegal links; she tried to blackmail him into staying with her with that knowledge, but he shot her dead.
- Hello, Attorney!: Kinshiro could be said to be one, since he is a magistrate in his day job.
- Hospital Hottie: Wakasa's day job is being a doctor.
- Hot Librarian: Natsume's day job is managing his own bookstore.
- Honey Trap: Yui plays this role once in Aoi's route, disguising herself as a maiko to spy on Tori and Willem. Bad thing, while she gets the info needed, Willem realizes it's her.
- I Kiss Your Hand: One of the CG's has Willem taking Yui's hand and leaning in as if to kiss it, looking into her eyes.
- It's Personal: In Aoi's route, he and Yui are very angry when Chidori is murdered and pretty much swear to find who did this to her.
- Local Hangout: The Kyoukatei tea house, handled by Kinshiro in addition to his magistrate job. It's also the place where those who need the Vigilantes can contact them if needed.
- Locked Out of the Loop: Ichika is actually the other Love Interest (aside of Willem) who isn't a member of the Edo Vigilantes. He only finds out in his route and some spin offs.
- Princely Young Man: One of the boys, Sion Iseya, is a guy from a very loaded family.
- Real Men Wear Pink: Aoi makes a living out of this trope, since he works as a stylist and hairdresser for courtesans and prostitutes. Hell, in his route, he and Yui bond over him doing her hair!
- Red Eyes, Take Warning: Soji has very prominent red eyes and is one of the most effective members of the Edo Vigilantes.
- Red Light District: Yoshiwara, the RLD of Edo, plays an essential route in this game since Aoi works as a beautician for the prostitutes there. Yui naively thinks that it's an example of the Liberal Type, but Aoi immediately shoots the idea down and tells her it looks Liberal, but is more of the Pitiful type underneath. The fact that Aoi's prostitute friend Chidori is murdered in broad daylight there confirms it.
- Replacement Goldfish: In Aoi's route, it's revealed that he had a younger sister, but he had to cut ties with her when he and Soji left their ninja village. He tells Yui about her and she wonders if thinks of her as a replacement, but at a certain relationship level he will say that he loves her for herself.
- Rose-Haired Sweetie: Yui is a kind, pink-haired young girl.
- You Gotta Have Blue Hair: Aoi has it, but the other Vigilantes have pretty spiffy hair colors too.