The earliest elevated rapid transit in New York was opened in the 1870s in Manhattan and in the 1880s in Brooklyn. New York and Brooklyn were two separate cities until 1898, and the first possibility of rail connecting them wasn’t until the Brooklyn Bridge opened in 1883. The layout of the rail systems reflected the different agendas of the people in the two cities. The four elevated lines in Manhattan ran basically north to south, to connect the growing residential neighborhoods in Midtown and to the north to the downtown business district. Brooklyn’s lines were arranged in more of a fan shape, to connect the outer areas of the city to the roughly-northwest downtown, but also specifically to make it easy for people to get to the East River ferries to Manhattan. A significant portion of the modern-day subway layout in Brooklyn is based on those old lines.
The photo above shows the M train at the intersection of Broadway and Myrtle Avenue – Brooklyn’s Broadway, which has no relation to Manhattan’s Broadway, or Queens’s Broadway or Staten Island’s Broadway – with an unused elevated line above it. There’s no great mystery here: two separate elevated lines were built long ago and one has been partially abandoned. The lower structure is the Broadway elevated, which connected Jamaica in Queens to the ferry that ran from the foot of Broadway to Grand Street in Manhattan. That ferry was eventually made obsolete by the construction of the Manhattan bridge, and the elevated rerouted to run over the bridge. The modern J train is the subway line that runs over the bridge and out to Jamaica. The upper structure is the Myrtle Avenue elevated, which originally ran from downtown Brooklyn out to Bushwick in Brooklyn and Middle Village in Queens. The west end of the line was later extended to a station at Park Row in Manhattan, running over the bridge and replacing the original cable-car shuttle. As built, the Myrtle and Broadway lines had a transfer (by taking stairs form one platform to the other) but no direct connection.
In 1914, a rail conenction between the two lines was built, allowing trains to travel over the Williamsburg Bridge and Broadway, and then switch to Myrtle Avenue to head northeast towards Bushwick. That’s the route of the modern M train. Here’s the connection:

The lower curving track is the connector, which then ramps up and joins the higher Myrtle Avenue track structure. Here’s the ramp:

The portion of the Myrtle Avenue el west of Broadway was abandoned and demolished in pieces between 1944 (when elevated service over the Brooklyn Bridge ended) and 1969. Newer subway lines had replaced part of the service, although people near Myrtle Avenue and the Brooklyn Navy yard are less-well served by transit than they used to be. In any case, here’s the unused stub of the Myrtle line immediately west of Broadway:

You can tell it’s unused, knowing nothing of this history, because there are no cross-ties above big girders that supported the rails.
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