The bright-pink ninja-emblazoned train isn’t exactly the epitome of stealth as it cuts through the forested hills and rice paddies of Mie Prefecture. Neither are visitors’ pint-size offspring who race excitedly up the paths of Ueno Park in the city of Iga shrieking their excitement at the prospect of getting up close and personal with fun and fear in the shape of Japan’s famed spies and assassins of history and legend.

What awaits us all at the Iga-Ryu Ninja Museum may not be quite the real deal, but the town is determined to hang on to its storied — if rather shadowy — past.

Long before the word “ninja” was hijacked for a bunch of masked mutant turtles, these masters of secrecy and disguise were an actual part of Japanese feudal society. Yet the art of ninjutsu (the Way of Stealth) is not indigenous to Japan. The ancient discipline is rooted in spiritual principles from the Indian subcontinent, and tempered by a healthy dose of mysticism and Buddhist asceticism brought to these shores by Chinese warrior monks.

The form of ninjutsu we inhabitants of the modern world would recognize, both a belief system and a range of combat techniques, evolved to its current form sometime in the Heian Period (794-1185) that also witnessed the flowering of aristocratic niceties so well conveyed in its best-known tome, “The Tale of Genji.”

Ninja rose to prominence in the 12th century as the nation’s samurai class steadily gained power. A ninja’s willingness to use poisons, sneak attacks and other guerrilla tactics that generally ran counter to the samurai’s chivalrous, honor-driven code of bushidō (the Way of the Warrior) made them extremely popular as hired “special forces” operatives of their day.

They became particularly active during the Sengoku (Warring States) Period of continuous tumult and conflict spanning some 150 years from the middle of the 15th century, when feudal daimyo lords would tap ninja to spy on their enemies and carry out nighttime raids.

Ninja back then were also known users of gunpowder, which they had managed to manufacture without the usual necessary ingredients from abroad. Their knowledge of this military game-changer was a closely guarded secret and most ninja homes were replete with nooks and crannies wherein both the black powder itself and any information regarding its creation and use could be safely stored and protected.

In fact, the front half of the Iga-Ryu Ninja Museum is a perfect example of a “ninja house” — a dwelling that looks typical from the outside but hides a host of secrets within.

Though the house comprises a mere three tatami-floored rooms looking out over carefully raked dry gardens with pleasing selections of greenery, as our guide Yuki showcases hidden passages and disappears behind doors in the blink of an eye, I soon discover it’s not your typical dwelling.

For instance, as we train our gaze on a seemingly impenetrable wall, Yuki illuminates a costumed ninja figure hiding in a crawl space between floor levels. Then, in the corner of a bare alcove, she flips a latch to reveal a passageway that leads out from beneath the family altar and emerges in a well.

Meanwhile, at the back of the house, lifting the bases of sliding shoji-screen doors exposes sandpits for hiding scrolls and other valuables. Nearby, when an ordinary-looking floorboard is levered up, a cache of swords and shuriken (throwing stars) sparkle below. In a clever touch, even the English explanatory scrolls here are concealed; after each demonstration, Yuki tugs on a string and the panel on which they’re displayed disappears into a wall.

The guided part of the tour is brief, but a stone staircase leads underneath the house to a continuation of the exhibit. It’s here that most of my preconceptions about ninja are shattered. For one, it seems that black was not the preferred color for their shinobe shōzoku (typical outfits), since it apparently struck too clear an outline in shadowy places. Rather, the ninjas of Iga dressed in navy-blue garb that was dyed for them by local farmers.

However, ninja would often adopt disguises — typically as one of seven general identities, ranging from farmers or itinerant priests to acrobats. Though it was easiest to hide weapons in the folds of a priest’s robe or a farmer’s attire, it seems they often strapped their shuriken to their shins, where they were both easy to grab and could deflect blows to a vulnerable part of the body.

Just as I am stepping off a pair of mizugumo — huge circular wooden “feet” that ninjas would don to walk across swampy moats or brackish bodies of water — a bell signals that showtime at the museum is about to start.

Like many productions staged for tourists, there’s some cheesy music and “humorous” antics — but the ninjutsu skills demonstrated by the performers are impressive nonetheless.

One of the female warriors takes down her opponent with a tricky rope maneuver while her male colleague demonstrates deadly accuracy with his shuriken, burying first one, then two, and finally three of the metal disks at a time in a thick wooden plank. After the show, costume-clad youngsters line up to try their hand at the throwing stars, while I choose to sniff out a bit of welcome sustenance.

Ninja were known to avoid strongly flavored foods for fear of discovery by keen-nosed enemies, but I have no such qualms as I follow wafts of delicious smells to a rustic-looking restaurant just outside the museum walls. The menu is a standard selection of noodles — both soba and udon — but I choose to top the latter with shreds of Iga beef, which locals claim is just as delicious as the famed cuts from nearby Kobe. I’m not disappointed; even the beef on a ¥900 bowl of noodles is rather succulent and I struggle not to gobble it up before I’ve even touched the doughy noodles beneath.

After lunch, I climb up the cobbled path near the Ninja Museum for a close-up view of Iga Ueno Castle, a gleaming white beacon visible for miles across the surrounding plain. Like so many of Japan’s feudal castles, this is a replica of the original wooden structure destroyed in a typhoon in 1612. Unlike its brethren, though, this edifice — standing since 1935 — survived the bombings of World War II.

I skip the inside of the castle because, to my mind, they’re usually fairly dull — and besides, I’m more interested in the original, vertigo-inspiring 30-meter walls that surround it and are the highest of any fortification in Japan. There are no real safeguards in place other than a thigh-level stone wall, so I sneak a peak at the dizzying drop. These walls are famous — Akira Kurosawa featured them in his 1980 movie “Kagemusha” (“Shadow Warrior”). I try to imagine a troop of ninja scaling the edifice with sure feet and a few hooks. It’s an easy mental picture to paint.

Back on the far side of the park, I pop into the Basho Memorial Museum. Japan’s most famous haiku master, Matsuo Basho (1644-94), was born just a short walk from Ueno Park and many of his travel journals are on permanent display here. I’ve been known to appreciate a good haiku when the mood is right, but the exhibit is small and, disappointingly, untranslated. To supplement the experience, I attempt to visualize Basho as a ninja. This second daydream, though, is less successful.

Back in the train station I notice for the first time the handful of ninja scattered among the platform’s rafters. Despite their Crayola-colored costumes, I somehow missed spotting them on arrival. But perhaps, like the real shadow warriors of Iga before them, they’re just masters of that great ninja art of hiding in plain sight.

Iga-Ryu Ninja Museum (open daily 9 a.m.-5 p.m.; adults ¥700) and Iga Ueno castle are both in Ueno Park, a short walk from Ueno-shi Station in Iga, Mie Prefecture. From Nagoya, take a Kintetsu Limited Express, switching at Iga-Kambe to the Iga Line (¥3,150 and two hours each way).

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