At East New York the line rises to street level to cross above the north-south, freight-only Bay Ridge Branch, then descends underground once more.

Between East New York and Jamaica, the closed but intact station at Woodhaven Junction is visible.

At East New York the line returned to grade level then rose onto another elevated viaduct until Atkins Ave.

For a while the LIRR operated joint service along the Atlantic Branch with the Brooklyn Rapid Transit company (BRT) consisting of two connections, one with the Fifth Ave El at Flatbush Avenue, and another with the Broadway and Lexington Avenue els with a connection built at Chestnut Street in Brooklyn.

This allowed BRT trains to access the Rockaways and Manhattan Beach, while affording the LIRR a connection into Manhattan to the BRT terminal located at Park Row over the Brooklyn Bridge (this service predated the opening of the East River Tunnels to Penn Station).

On December 28, 1942,[3] the tunnel was completed and opened with the two remaining at-grade tracks pulled out of service.

Around this time Atlantic Avenue was raised over the East New York station via a viaduct that separated the road and the railroad.

The elevated trestle from East New York to Atkins Avenue was also demolished as it had been included in the new tunnel to Jamaica.

This change took effect June 25, 1876, and resulted in the closure of the South Side's Berlin, Beaver Street (Jamaica), Locust Avenue, and Springfield stations.

Other trains traveling east of Jamaica run to Penn Station, Grand Central Madison, or Long Island City.

[9][10] Media related to Atlantic Branch (Long Island Rail Road) at Wikimedia Commons