Formerly operating along most of the south coast region (including all lines on Cape Cod), Bay Colony's final operations ceased in late 2023, when the only two remaining lines (a roughly six-mile stretch of track between New Bedford and Westport, referred to as the Watuppa Branch, as well as a section of the Millis Branch from Medfield Junction to Millis) were purchased by Massachusetts Coastal Railroad.

In addition to moving freight for its customers, Bay Colony also performed AAR-certified repairs on rolling stock and contract track construction projects for other railroads.

[3] The contract for the railroad lines owned by the State of Massachusetts administered by the Executive Office of Transportation (EOT), which included the Cape Cod main expired on December 31, 2007.

[6][7] However, on December 15, the Surface Transportation Board (STB) rejected the transfer of Millis Branch operations due to uncertainty about the status of the line.

[8] Mass Coastal announced the purchase of the Bay Colony was final in February 2024, excluding the Millis Branch which remained held up by legal issues.