From the Super Mario Wiki
The Soybean civilization, whose people have also been collectively referred to as the "Soybeans", was an ancient civilization that once inhabited the Beanbean Kingdom. Most of the Soybeans' past (and even their existence, which is only verified by the Beanstones and other remnants) is an enigma, and they were only hinted at in Mario & Luigi: Superstar Saga. Even hearing about the Soybean civilization is completely optional for the player, but they can do so by talking to Fava's brother (who describes himself as a great intellect) in Beanbean Castle Town, unless the town is under attack by Cackletta. If they do so, he will inform them that he is currently most interested in studying the Soybean civilization and will ask Mario and Luigi if they wish to hear a report on it. If they answer "Yes", then he will begin speaking of the civilization, revealing much about it.
Apparently, the Soybean civilization had at least three components: spin-beans (who had the ability of flight, likely a reference to the Spin Jump), mole-beans (who, like any other type of mole, could dig through the ground), and dash-beans (who could move at super speeds, hence their name). According to the intellect, the Soybeans may have also very well lived in the Beanbean Kingdom (or maybe even Beanbean Castle Town itself), although the only possible proof of this would be the location of the ten Beanstones, the civilization's buried treasures, in the town. The Mario Brothers could then accept the man's challenge of locating these underground gems, and he would finally reveal that the Soybeans were extremely short; as such, only Mario's crushed form could find the otherwise invisible Beanstones. (When the small Mario stood on one of the invisible pits in which the gems were placed, an exclamation point would appear above his head and, if Mario & Luigi: Superstar Saga was being played on a Game Boy Player, the GameCube controller would rumble.)
Afterwards, a Toad in Little Fungitown would state that the lift platform from Teehee Valley to Little Fungitown was built by the people of the Soybean civilization; the design of this platform (which sported many fancy Mushrooms) may suggest that the Soybeans had some connection to Toads. These were the only mentions of the advanced bean civilization and even when Mario and Luigi found the Beanstones and took them to Fava's aforementioned brother (who rewarded them with a Bros. Rock badge), he would only claim that he would announce his hypothesis on the civilization and take no further action in-game. Finally, it may be worth noting that, while references to the Soybean civilization are rare in Mario & Luigi: Superstar Saga, the invisible pits in which the Beanstones are stored (as well as the strange reactions they trigger in short people) were actually spoken of in one of the many books belonging to a separate character in Beanbean Castle Town.
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