In the near-future, a Mega-Corp called the Mars Corporation led by a supervillain called Spider is researching illegal technology and attempting to create assorted superweapons. Three members of the elite ninja commando force - Ryu Eagle, Joe Tiger and Rayar Dragon - is sent to investigate.
After battling their way through the Mars Corporation's security forces and taking down their private army, the ninja commandoes prepares to confront Spider, only for Spider to escape into a time machine and flee through time. The ninja commandoes managed to hijack a prototype time machine of their own and gives chase, leading to a series of levels in Feudal Era Japan, Ancient Egypt, Warring States China, the Age of Dinosaurs and Europe in the 1940s as they wipe out Spider's bases and stop the villain from rewriting history to prevent his present-day defeat.
"You guys have driven me completely mad!" — Spider
- Animal Theme Naming: The ninja commandoes are respectively named Ryu Eagle, Joe Tiger and Rayar Dragon.
- Beethoven Was an Alien Spy: Thanks to Spider repeatedly screwing with time, Tutankhamun was a robotic pharaoh overlord, Lu Bu was a weredragon, and Oda Nobunaga a giant cyborg swordsman.
- Big Bad: Spider, leader of the Mega-Corp known as Mars Inc., who is developing illegal superweapons to Take Over the World. When the ninja commandoes confront him, he then escapes through time to reset history, and the heroes must stop him.
- "Blind Idiot" Translation: The game's English translation isn't accurate, to say the least. You know the quality of the transcript you're getting when the opening briefing contains this gem:"Go investigate and ruin his plans light now!"
- Book Ends: The first and last stage is set in the Mars Corporation's headquarters. You begin by raiding Spider's hideout, only for him to escape via Time Machine where you then chases him through time, and after a series of levels across multiple time periods where you repeatedly thwart Spider's attempts to rewrite history. After defeating him for good in the 1940s, though? The headquarter's supercomputer is still active and you need to return to the first stage to wipe it out for good.
- Boss Rush: In the last stage when you finally attempt to shut down the Mars Corporation for good, it's supercomputer will re-use it's time machine to teleport multiple past bosses into the present, which you must defeat again. Firstly Tutankhamun, then Lu Bu, then the dragoni-like dinosaur boss, and finally the supercomputer's core.
- Collision Damage: All over the damn place. The commandoes lose health merely from touching mooks and enemies, while the bosses can remove entire chunks of the player's health just by gently bumping into them.
- Cores-and-Turrets Boss: Fittingly enough, the Mars Corporation's core and the game's True Final Boss, a single core surrounded by multiple turrets and guarded by two massive, swinging robot arms trying to squash you to a pulp.
- David Versus Goliath: The bosses are huge compared to the ninja commandoes. Even the human-based bosses like Lu Bu, Oda Nobunaga, the sumo wrestlers, mummies trio and the caveman giant absolutely towers over the protagonists.
- Dinosaurs Are Dragons: The Prehistoric Era have you battling a dinosaur boss with draconic features, including dragon's frills, horns, and the ability to breathe fire, where it's pretty much a wingless dragon without being referred by name. Though it's subverted by the Robotic Reveal.
- Dual Boss: Most levels have dual or triple Mini Bosses halfway through that must be defeated before facing the actual boss. Like the two Sumo wrestlers, three mummies, and tanks in 1940s Germany.
- Famous Ancestor: Ryu Eagle, the older male playable hero, is a 23rd descendant of Fuuma Kotaro.
- Fake-Out Fade-Out: The last time-travel-themed stage, Europe in the 1940s, ends with the ninja commandoes finally confronting Spider, and defeating him for good. The following cutscene actually have Spider caught in a fiery explosion and blowing up in a blaze of glory, as Joe declares "we finally did it!", looking a lot like the victorious final scene of so many old arcade actioners. But then Ryu, in the same scene, said the Mars Corporation still exists in the present owing to their supercomputer still in control. Cue the final stage.
- Fighting Across Time and Space: Barring the first and last stage, most of the game have Spider escaping to different time periods with the intentions of rewriting history, and the heroes reaching a different era only to find out Spider had established his hideout and have a legion of his minions awaiting in ambush. They then defeat Spider's underlings before confronting Spider, only for the villain to escape into another era, rinse and repeat until the final stage that goes back to the present.
- Fire-Breathing Weapon: The 1940s stage have you facing German soldiers armed with flamethrowers. You can also collect a magic version of this trope with the fire spell, which turns your energy projectiles into a stream of flames.
- Flunky Boss: Practically all bosses (except the sumo wrestlers and mummy trio Mini bosses) have plenty of mooks assisting them. The caveman boss can even turn his mooks into projectiles (see below).
- Grievous Harm with a Body: The gigantic caveman boss in the Prehistoric level starts his battle by grabbing an unfortunate passing nautilus and uses that as a club. You manage to relive him of his weapon, but then he'll summon lesser cavemen enemies and occasionally, if a caveman mook is too near the boss, he'll grab said mook and throw him at you.
- Incredibly Durable Enemies: The amount of punishments human mooks can absorb in later levels are insane. Even regular enemies like cavemen, Chinese soldiers, and ninja can tank four to eight arrows, shuriken or projectiles before they expire. Should you get surrounded without upgrades increasing your attack power and the game will kick your ass. Though it makes sense with one cutscene revealing them to be androids.
- Losing Your Head: Lu Bu, the boss of Three Kingdoms-Era China, detaches his head as his body dies. His head then floats around, taunts you and suddenly turns into a Chinese . He does that again in the final stage when Spider calls in a Boss Rush and he's one of the returning bosses.
- Man-Eating Plant: Giant fanged flowers appears in the prehistoric stages, and can gobble you up instantly if you get too close.
- Man on Fire: Enemies hit by flaming attacks, either fire spells, Arrows on Fire from Rayar, Joe's flaming dragon move, and other fiery projectiles will instantly turn into a human-shaped pile of flames before roasting to dust. You have a burning death animation yourself too should you be killed by fire (e.g. torched by a Chinese dragon).
- Make Wrong What Once Went Right: Pretty much the entire M.O of Spider, right into the first stage; as the ninja commandoes raid his headquarters, Spider then leaps into his prototype time machine and escapes into the past to rewrite history so his present-day defeat doesn't happen. The commandoes managed to capture a second time machine, and pursues Spider and his minions across a number of eras.
- McNinja: Joe Tiger, an American member of the ninja clan and Rayar Dragon, who is British if that counts.
- Multishot: Rayar, unlike her male comrades, uses a bow instead, which she fires four arrows at a time by default. Upgrading her attacks allows Rayar to spam around ten arrows at a time. And Arrows on Fire for good measure!
- Mummy: Three of them shows up in ancient Egypt as a Mini-Boss trio.
- Ninja: Well, in a game called Ninja Commando... besides the titular trio, the stage in Edo-Japan have ninja as enemy mooks.
- Palette Swap: On two-player mode, you and your partner can actually play as the same commando. For instance, both players selecting Joe Tiger will have two Joes onscreen wearing red (P1) and blue (P2).
- Playing with Fire:
- All three of the commandoes have access to fire-based attacks, including fire spells, creating flaming dragons incinerating onscreen mooks, and the like. Rayar especially can spam fiery attacks both in front and on her sides, fitting her motif.
- Tutankhamun can release hordes of fireballs at the commandoes.
- The Chinese dragon boss (who used to be Lu Bu) and fire-breathing dinosaur, expectedly.
- Robotic Reveal:
- At the end of one stage after the commandoes defeat all the mooks Spider threw at them, Rayar picks up a severed arm and notices the wiring sticking out from the inside. Ryu deduces that Spider have been replacing his life-like androids into the populations of ancient civilizations to reshape history.
- The dragon-like dinosaur boss is actually a robot, losing skin from it's forelimbs and face as the battle goes on with it's interiors being a Mechanical Monster.
- Sequential Boss: Both of them which starts off the same size as your heroes, but then turns gigantic when you defeat them the first time:
- Oda Nobunaga starts by sending ninja mooks at you, and hurling ranged projectiles via his Combat Hand Fan combined with a Spin Attack. You then defeat him only for Nobunaga to transform into a giant in samurai armour, holding a massive katana with Sword Beam abilities.
- Lu Bu is already giant-sized when you first fight him, but when you defeat him, his body dies... but his head detaches, turns into a Chinese dragon, and continues fighting with a new health bar.
- Shaping Your Attacks:
- The two male ninja heroes, Ryu and Joe, can fire flaming projectiles shaped like eagles.
- Lu Bu has an attack where he hurls energy blasts shaped like burning skulls. Oda Nobunaga have a similar one he launches from his sword, shaped like a tiger's head.
- Smart Bomb: All three of the ninja heroes can execute a special attack that damages all enemies onscreen when their power meter is high enough, and deal a crippling blow on bosses. Rayar's being a massive flaming tornado, while Joe and Ryu lets out a spinning circle of energy blades.
- Spread Shot: Ryu and Joe can obtain power upgrades where their flung projectiles spreads out into arcs of up to a dozen at a time.
- Sumo Wrestling: Two huge-but-acrofatic sumo wrestlers appears as a mid-boss in ancient Japan. Beware their Spin Attack which throttles away your health within seconds!
- Sword Beam: Oda Nobunaga from Edo Japan can repeatedly spam energy projectiles from his sword. Either as crescent-shaped waves, or as a thick energy blast.
- Time Machine: The first stage have Spider escaping in one to avoid the ninja heroes. And then the commandoes managed to hijack a second machine and pursues Spider through time.
- Two Guys and a Girl: Joe Tiger and Ryu Eagle are the guys, Rayar Dragon is the girl.
- Spider's and Mars' scheme has been wiped out.
This is the finale. The battle throughout the ages seems to come to an end.
But remember, it is not equal to the coming of peace.
Peace in the future should be built by your hands.END