The second portion, from Jefferson Street to Ridgewood, was leased from the Brooklyn and Rockaway Beach Railroad Company, and was known as the Evergreen Branch, a name later extended to the rest of the line.

With passenger service over, the remainder of the line between South Side Crossing and Cooper Avenue became exclusively used for freight.

While parts of the branch's right-of-way have been built upon in recent years, parking lots, newer buildings, and old rails, show where the line formerly went.

[4][5]: 2, 6 The Evergreen Branch's original northern terminal was at Quay Street in Greenpoint along the East River, where passengers transferred to and from ferries to Manhattan.

From there, it crossed Metropolitan Avenue, Grand Street, and a portion of the Newtown Creek with a small bridge[dubious – discuss].

[failed verification][6] The tracks dipped slightly southward at Cornelia Street before going back to the regular alignment.

[6] From there, the line proceeded southeast and connected with the Bay Ridge Branch at Cooper Avenue Junction near the Cemetery of the Evergreens.

[7][8] The origin of the Evergreen Branch traces back to the Glendale and East River Railroad (G&ER), which was incorporated on March 26, 1874,[9]: 38 [10] to build a railroad from Quay Street in Greenpoint, Brooklyn to Huntington on Long Island, running through Glendale, Queens.

The idea for a line to Greenpoint reemerged when Austin Corbin proposed the New York & Manhattan Beach Railway Company (NY&MB) to connect his resorts in Manhattan Beach with New York City via ferry service in Greenpoint.

The new line ran between from Cooper Avenue Junction to the Montauk Division at Fresh Pond, opening on June 2, 1883.

In order to maintain service to Greenpoint, a shuttle was operated to connect with the Manhattan Beach trains at Cooper Avenue Junction in Bushwick.

[22]: 92 [23] In April 1886, service to Greenpoint was abandoned due to the expiration of the eight-year lease for the Quay Street station and facilities.

The LIRR, with its new terminals at Flatbush Avenue and Long Island City available, did not see any reason to pay $6000 a year in rent for an unneeded facility.

[21] Freight traffic started to significantly decline in 1938,[31] and on February 9, 1939, eight blocks of track, totaling 1,834 feet (559 m), were removed between Starr and Himrod Streets.

[6] By the late 1970s, the Cooper Junction end of the line only had one remaining customer: Tulnoy Lumber, located at Putnam Avenue.

[33]: 64  However, the Interstate Commerce Commission (ICC) postponed authorization for abandonment to review offers from the Long Island Rail Road and the New York State Department of Transportation (NYSDOT).

[32] Portions of the Evergreen Branch near the former location of the Cooper Avenue Junction are still owned by the Long Island Rail Road.

[42] Some stretches of abandoned track persisted for several years: in 2000, the website Forgotten NY documented several instances of trackage that remained both on streets and in lots along the right-of-way.