BostInno is reporting (via a post within the Eater forum) that John Moore of Navy Yard Bistro was looking to open a place called "Nickel" in the historic Five Cents Saving Bank building in Thompson Square (near where Main Street and Austin Street meet), but he says that his proposal was denied and a location of Starbucks will now apparently be moving into the spot. The article mentions that Moore's eatery was going to be a "swanky" place with sushi, a burger bar, and some Thai fare, but he indicated that such a restaurant would need more investment in the building than a coffee shop would, which may be why Nickel lost out to Starbucks.
Navy Yard Bistro first opened its doors by 1st Avenue and 6th Street a bit more than a decade ago.
[November 4 update: It appears that John Moore's proposed restaurant has indeed lost out to Starbucks, as a licensing board page indicates that Starbucks has applied for a common victualler license to operate within the Thompson Square space.]
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[A related post from our sister site (Boston's Hidden Restaurants): List of Restaurant Closings and Openings in the Boston Area]