After pleas from the local community and transit advocacy groups, the MTA agreed to spend $74 million to rehabilitate the line.

[2][3] The Brooklyn, Flatbush, and Coney Island Railway (BF&CI), which built the Brighton Line, was incorporated in 1877 in order to connect Downtown Brooklyn with the hotels and resorts at Coney Island, Manhattan Beach, and Brighton Beach.

[5]: 90  Therefore, the line was to be built in a trench through the hill in Crown Heights, connecting with the tracks of the Long Island Rail Road (LIRR) at Atlantic Avenue.

The route was built on the surface between Bedford Terminal (at Atlantic Avenue) and Park Place, and was built in an open cut to Prospect Park and beyond to Church Avenue in Flatbush in order to avoid grade crossings and to placate the local community.

[7][8][9] Later on, in order to accommodate larger locomotives for LIRR through-service, the open cut had to be dug deeper.

[5] However, the LIRR later gained control of the New York and Manhattan Beach Railway, a competitor of the BF&CI, and on December 14, 1883, ended the agreement to provide equal access to the Flatbush Avenue Terminal.

[12] The connection linked to the Fulton Street Elevated, which ran from Downtown Brooklyn to City Line at the border with Queens County at Liberty and Grant Avenues and had been completed in 1893.

[7] Brooklyn and Brighton Beach Railroad trains continued to run from Bedford Terminal, but this service was soon abandoned, though the track connections were retained.

Trains that used third rail in elevated service raised trolley poles at Franklin Avenue station.

In the ensuing years, some existing bridges were strengthened or replaced and some of the elevated trackage was placed on concrete-retained embankment.

[7] A series of leases and mergers at the beginning of the 20th century ended the independent existence of a number of elevated and suburban railroads, including the Kings County Line and the bankrupt Brooklyn and Brighton Beach.

The new city turned its attention to subway building and the Interborough Rapid Transit Company had a leg up in landing the first two contracts.

A five-car wooden elevated train, heading southbound along the Franklin Avenue Line passed the Consumers Park station without stopping, left the tracks and crashed into one of the new tunnel walls, killing 97.

[18][2] At the same time, track connections to the Fulton Street Elevated were severed so that through service to Brooklyn Bridge was no longer possible.

South of Prospect Park, there are switches between all four tracks, allowing southbound trains from either line to run either local or express to Coney Island, as well as permitting northbound local and express trains from Coney Island to access either line.

For the summer excursion season of 1924, the Franklin Avenue Line was upgraded for the operation of six-car subway trains, and was assigned the BMT number 7.

[15]: 98  A crosstown line would eventually be built in the 1930s; however, it was part of the city-operated Independent Subway System, not the BRT.

As a result, most trains avoided negotiating the sharp S-curve where the Malbone Street Wreck had occurred.

A major blow to the viability of through-service occurred in 1954 when the D train of the IND Division was extended to Coney Island via the Culver Line, deprived the Franklin of a major source of transfer traffic, consisting of passengers from Harlem and the Bronx, who now had a more direct route to Coney Island.

In 1985, when the practice of using double letters was eliminated, this service became the S.[15]: 98 [23] On December 1, 1974, a southbound shuttle train of R32s was approaching the tunnel portal en route from Franklin Avenue when it derailed on the crossover and smashed the same place where BRT car 100 had hit in the Malbone Street Wreck.

This derailment resulted in some injuries, but there were no fatalities, because time signals limited the speed of trains coming down the hill from Crown Heights.

[15]: 98–100 In January 1977, the Metropolitan Transportation Authority (MTA)'s Emergency Financial Control Board proposed abandoning the severely deteriorated line due to cutbacks in city funding.

They were aided by Congress members Shirley Chisholm and Fred Richmond, who issued a statement in support of the riders of the shuttle, including 2,000 students.

[28] In 1986, the New York City Transit Authority launched a study to determine whether to close 79 stations on 11 routes, including the entire Franklin Avenue Line, due to low ridership and high repair costs.

[29][30] Numerous figures, including New York City Council member Carol Greitzer, criticized the plans.

Shuttle trains' lengths were shrunk from four to two cars, and the platforms were so poorly maintained that they were literally crumbling.

They argued that subway station repair work occurred elsewhere, when no attention was paid to the Franklin Avenue Shuttle.

[36] As a result, most of the supporting infrastructure and stations were completely rehabilitated for eighteen months, between July 1998 and October 1999 at a cost of $74 million.

[33] The local community agreed to close the station in exchange for the construction of a new passageway to provide transfers to the IRT Eastern Parkway Line at Botanic Garden.

[42][43] Once the line was reopened there were still calls to restore the Dean Street station, and there were complaints that the Botanic Garden and Prospect Park stops were not made ADA accessible.