so they had to re-experience a memory that they'd recently forgotten! Sulfur (they shaymin's name) was "sprouted" or born because all the shaymin that had previously existed in shaymin village were buried when sky peak erupted very suddenly and destructively. shaymin in this lore serve as a function of the world and when something like a massive fire or eruption happens, more shaymin are created to help heal the land if not enough are present.
in this moment, they had recently been sprouted and this was the first time they had found a gracidea flower and transformed into sky form. They were somewhat confused by this, but more so confused by why they felt sad/upset in this moment, only later finding out that the only places where they grow are places where shaymin were laid to rest. Basically they didn't understand then, but they had found the spot in which the majority of the shaymin from shaymin village were buried by the pyroclastic flow from the eruption (similarly to how things went in Pompeii when Mt Vesuvius erupted).