A malodorous stench emanated from the Neponset River in Boson and Milton Wednesday, as thousands of dead fish — the victims of a massive “die-off” — stacked up on the shorelines. © Jesica Binaldi/Boson Globe Staff Dead fish are seen as they collect against the Amelia Earhart Dam in the Mystic River. It’s a scene that has replayed in these waters at least twice over the last four years, and officials say the cause, while unfortunate, is natural. The creatures are menhaden, more commonly known as “pogies,” a fish that travels in large schools by nature, according to Patrick Herron, executive director of the River Watershed Association. It’s likely, Herron said, that a school of the fish was driven from Boson Harbour into the Neponset River by a predator, like a striped bass, or striper. Once in the river’s shallow and warmer waters, he said, the fish probably stuck around too long and depleted the oxygen supply, leaving them to suffocate by the thousands. “They came in in suc...