On October 2, 2008, the state government announced an agreement with CSX Transportation for the purchase and upgrade of several of CSX's freight lines in the state. CSX agreed to sell the Fall River Secondary and New Bedford Secondary for use by the South Coast Rail project, as well as the Grand Junction Branch, the Framingham-to-Worcester section of the Worcester Line, and the South Boston Running Track. Other parts of the agreement included plans for double-stack freights west of Worcester and the abandonment of Beacon Park Yard.[7] The agreement was signed on September 23, 2009.[8] On June 11, 2010, the state and CSX completed the first phase of the agreement, including the transfer of the South Coast Rail lines to MassDOT; the Massachusetts Coastal Railroad assumed freight rights on the two lines.[1] The two lines were sold for $21.5 million.[9]
In May 2020, MassDOT issued a construction contract for the Fall River Secondary. The work included construction of Freetown station and Fall River station, 12.1 miles (19.5km) of track work, rehabilitation of 10 grade crossings and 8 bridges, and construction of Weaver's Cove layover yard in northern Fall River. Construction was estimated to take 30 months.[10][11]Fall River/New Bedford Line service began using the route on March 24, 2025.[12]