In a small castle on the side of Mount Moon, a peasant boy with only a Kabuto (who were not yet extinct, merely severely endangered) was handed a poorly made sword and shield and sent off to fight for his lord in another of the many skirmishes of the Sengoku era. The armies met one another, samurai and pokemon alike trading blows, and the peasant boy's small height and inexperience made him a poor soldier. As a katana came down towards his unprotected head, his Kabuto crawled up his back with amazing speed and blocked the attack with its shell. The peasant boy stabbed his assailant in the legs, and his short height and dexterous "helmet" enabled the Kabuto to block all the blows, saving his life in the process.
To maintain its grip, the Kabuto's claws had dug into his skull, and it could not remove itself without causing life-threatening damage. The boy became a man known for his skill as a soldier, then seized a castle for himself and won battle after battle until he finally became shogun, all with a pokemon on his head. His men copied him, capturing Kabuto of their own and wearing them as helmets until there were no more left to capture.
The rest, noting the fine protection (and high status) the real thing offered, asked craftsmen to make Kabuto-shaped helmets in the hopes of capturing some of their defensive power. In time, they replaced the real thing entirely, for before long there were no more live Kabuto left. And even today, when one thinks of a samurai helmet, they think of ones in the shape of a Kabuto.