With the destruction of Akuma's criminal underworld and Takeshi gone, the mysterious and murderous Mr. Haruto rises from the ashes and takes charge of the criminal underworld. Meanwhile, a seemingly ordinary guy named Kichiro receives a message to go to a special Zen garden, where a hologram of his real father - Takeshi - reveals that Kichiro is destined to become the next Final Ninja. Kichiro dons the suit, and fights against Mr. Haruto's forces.
The gameplay is very similar to the last two Final Ninja games, with similar obstacles and structure of levels and platforms. The controls are the exact same: [Up or W to jump, Left or A for left, Right or D for right and Down or S for stealth] as well as using the mouse to throw shurikens.
Unlike the previous Final Ninja games, Final Ninja: Nextgen is multiplayer, provided you have passed the first five levels on your own first. On Level 06, Kichiro can be joined by his friends.
Yuto is Kichiro's closest companion, who has the special ability to summon and shoot balls of dark matter, and is able to blend in with the shadows. His dark powers are apparently the result of being experimented upon as a child by Evelyn.
Elizabeth "Lizzy" Ohno is a skilled samurai who was previously employed by Mr. Haruto, but decided to leave his gang because she felt that Haruto was 'too crazy for his own good'. As well as being able to deflect bullets with her samurai sword, Lizzy can cross through security laserbeams without an alarm being set off, possibly due to her association with Haruto.
Melody "Mel" Merlock is a girl who has a crush on Kichiro. She has expressed that she thinks Kichiro is sweet, and on one occasion, 'yummy'. She wields a gun that shoots green energy, which can be used to electrocute and therefore dispatch enemies, or it can be used to control enemies.
Reginald can be played as in Level 10, and also between Levels 16 to 18. Similar to Lizzy, he can pass through security systems without alarms going off. He also has the ability to throw daggers at enemies.
Level 00 - Prologue
Ever since the destruction of AKUMA and the final battle of TAKESHI, the criminal underworld had crumbled. That is until the mysterious and murderous MR. HARUTO rose from the ashes and took charge, becoming the new criminal kingpin. In the year 2078, a seemingly ordinary fellow by the name of KICHIRO discovered his true destiny...
Kichiro is in the city when he gets a message telling him to go to the Zen garden in exactly one minute. Kichiro must run through the city and dodge obstacles in order to get to the Zen garden in time.
After discovering his true destiny and donning the ninja suit, several enemies burst into the Zen garden and attack Kichiro, fearing the return of the Final Ninja. Kichiro must defeat these enemies before leaving the Zen garden.
Kichiro goes through the city, testing out new abilities like shurikens and stealth. There are more enemies to be defeated.
Shadow monsters arise from the darkness, and Kichiro must defeat them before they defeat him.
Kichiro arrives at Mr. Haruto's office at the docks, which is defended by shadow monsters as well as Haruto's personal samurai guard. When they're all defeated, a helicopter will rise from the office, containing Haruto. The enemies in the helicopter attack briefly, before fleeing the scene.
More shadow monsters appear and attack inside Haruto's office, where Kichiro finds Yuto, who had been brainwashed and forced into creating shadow monsters to fight Kichiro.
Kichiro and Yuto find themselves stalked by Mel Merlock, who decides to join their quest to combat evil. They also meet Lizzy Ohno, who also joins their cause. They fight a bunch of enemies together.
Kichiro and his gang descend into the sewers, where they are attacked by a bunch of robots.
More robots in the sewers, as well as a bunch of mutated rats.
Level 09 [Boss Battle: Evelyn]
Upon leaving the sewers, Kichiro and his gang find themselves being attacked by robots while Mr. Haruto and Evelyn dine in a room protected by a force-field, with Evelyn occasionally getting up and firing a gun into a portal, which leads into the battle grounds. Kichiro and his friends must fire into the portal while its open in order to hit Evelyn and knock her unconscious. Once the battle is done, Mr. Haruto and Evelyn will flee the scene.
Kichiro and the gang chase after Mr. Haruto, while many obstacles become in their way. Haruto eventually gets away, and they find Reginald imprisoned. When Reginald is freed, he will join their ranks and fight their way through enemies and robots.
Reginald is attacked and possibly killed by simian units in the junkyard that Kichiro and the gang stumble upon. They must fight these rogue simian units and escape the junkyard.
MR. HARUTO is a man who likes order. A world without order is a world filled with chaos and despair. He must get rid of the Final Ninja and his Followers for good! ... Suddenly an idea hits him like an angry chimpanzee. The only one who can defeat the Final Ninja, is the Final Ninja...
Kichiro and the gang are attacked by an army of Kichiro Clones. They must defeat these clones.
Kichiro and the gang must fight enemies, robots and avoid lasers in the big city.
Kichiro and the gang must fight enemies and avoid lasers in the big city.
Kichiro and the gang finally arrive at Mr. Haruto's base. They must avoid lasers, and then avoid the enemies that guard the building. Messages between Mr. Haruto and Evelyn can be read.
The heroes arrive in the Chemical Lab, which is where Evelyn is residing. Reginald is revealed to be alive and joins Kichiro's gang once more, helping them fight against the mutated test subjects in the lab. Evelyn is eventually found and attacks Kichiro and the gang, until she is defeated which results in her falling into a vat of toxic waste.
Rising higher in the Haruto base, Kichiro and the gang fight more samurai guards and enemies.
Kichiro and the gang face enemy mines and robots in the Robotics Laboratory where Mr. Haruto is reported to be hiding. However, "Mr. Haruto" just turns out to be a hologram. Suddenly Kichiro, Yuto and Mel are knocked out while Reginald starts laughing maniacally and puts on Haruto's signature mask, revealing himself to be Mr. Haruto.
Kichiro and the gang's first course of action is escaping the prison cells they were assigned to. Once they succeed in doing that, Kichiro and the gang must fight enemies, mines, robots, simian units, mutants and Kichiro clones before they reach the elevator.
Level 20 [Boss Battle: Haruto]
Kichiro and the gang arrive in Haruto's new office, where Haruto goes inside a giant mech and fights them. Kichiro and the gang must fight the mech, until it is destroyed and explodes.
And so, KICHIRO and his Friends have proven themselves to be capable heroes. This city doesn't need a ninja...it needs a Final Ninja, a Samurai Warrior, a Super Psychic and a Shadow Lord! Well done!
This slide shows Kichiro and his friends rejoicing, while a charred Reginald Haruto is being taken away by the police, revealing that he survived the mech's explosion although he is going to prison.
Meanwhile, deep in the Chemical Lab...
This slide shows Evelyn crawling from the vat of chemicals. Her hair has fallen off and her skin has become a sickly green colour. As she scrambles towards the door, she takes a fedora and a coat that are hanging from the wall as she flees the Haruto Base. Her coughs become less feminine and much deeper, and the last thing that is heard as the screen fades to black is the signature laugh of Doctor Nastidious.
- Reginald Haruto and Evelyn Nastidious are the main villains of this game. Ironically, it is Haruto's first name that gives away his identity and it is Evelyn's surname that gives away her identity.
- Given Evelyn's surname, which is revealed to be Nastidious if the game is completed and then played again, as shown by the messages sent from Evelyn to Haruto. During the first gameplay, the messages come up as "EVELYNN" which can just be assumed to be a spelling error. However, during a second saved gameplay, the messages are labelled "EVELYNNASTIDIOUS".
- Funnily enough, even though Haruto's first name Reginald is revealed, his messages are still labelled "MISTERHARUTO".
- Mel Merlock seems to be an obvious allusion to Maxwell Merlock, the main antagonist of Final Ninja Zero judging by her name, her food-related remarks about Kichiro "sweet" and "yummy", her weapon and her status as "Super Psychic" a term that Victor Boshi used to describe Maxwell.
- Mel could be a descendant of Maxwell Merlock.
- The name "Shadow Lord" used to describe Yuto is also the name of characters in Deltora Quest and Final Fantasy.
- Doctor Evelyn Nastidious' origins are similar to the Joker, a Batman villain. Both Evelyn and Joker fell into a vat of toxic waste which changed their appearance, and caused them to laugh crazily.
- Although Lizzy makes a comment about Haruto being crazy, he is actually never shown to do anything crazy. In fact, he is quite intelligent as well as calm and collected. He flees a battle whenever he knows he is at risk, disguises himself as an ally until the very end, and sets up a hologram.
- He does briefly laugh like a maniac, but probably due to some sense of sadism or, more plausibly, victory/success.
- This game proves that the Final Ninja trilogy takes place before the Test Subject series. This game shows the origins of Dr. Nastidious, who goes onto become the main villain of the Test Subject series.
- Until this game, Nastidious was originally thought to be male.
- There is a clue that Reginald is Mr Haruto. While thinking about a plan, an idea hits him "like an angry chimpanzee". In the previous level, Reginald is knocked unconscious by a simian unit. While recovering, Mr Haruto is also seen with a cane, which he didn't have before he was injured.