The full Second Avenue Line (if it will be funded) will be built in three more phases to eventually connect Harlem–125th Street in East Harlem to Hanover Square in Lower Manhattan.

[13] The long-term plans for the Second Avenue Subway involve digging 8.5 miles (13.7 km) of new tunnels north to Harlem–125th Street in Harlem and south to Hanover Square in the Financial District of Lower Manhattan.

72nd Street was eventually scaled down to a two-track, center island platform station in order to reduce costs,[21][22] A three-tracked 72nd Street station would have allowed trains from the Broadway Line to short-turn (reverse) without interfering with mainline service on Second Avenue, as well as provided additional operational flexibility for construction work and non-revenue moves.

[25][26][27] Turner's final paper, titled Proposed Comprehensive Rapid Transit System, was a massive plan calling for new routes under almost every north-south Manhattan avenue, extensions to lines in Brooklyn and Queens, and several crossings of the Narrows to Staten Island.

[25] In September 1929, the Board of Transportation of the City of New York (BOT) tentatively approved the expansion,[27] which included a Second Avenue Line with a projected construction cost of $98.9 million (equivalent to $1.74 billion in 2023), not counting land acquisition.

[29] In 1932, the Board of Transportation modified the plan to further reduce costs, omitting a branch in the Bronx, and truncating the line's southern terminus to the Nassau Street Loop.

The United States' entry into World War II in 1941 halted all but the most urgent public works projects, delaying the Second Avenue Line once again.

[34][35][27] The demolition of the Second Avenue elevated caused overcrowding on the Astoria and Flushing Lines in Queens, which no longer had direct service to Manhattan's far East Side.

[29][30]: 210–211  Another plan was put forth in 1947 by Colonel Sidney H. Bingham, a city planner and former Interborough Rapid Transit Company (IRT) engineer.

Reflecting public health concerns of the day, especially regarding polio, the R11 cars were equipped with electrostatic air filters and ultraviolet lamps in their ventilation systems to kill germs.

[25][32][41] Money from the 1951 bond measure was diverted to buy new cars, lengthen platforms, and maintain other parts of the aging New York City Subway system.

[49]: 37  The Second Avenue line was criticized as a "rich man's express, circumventing the Lower East Side with its complexes of high-rise low- and middle-income housing and slums in favor of a silk stocking route.

[60]: 52  In October 1974, the MTA chairman, David Yunich, announced that the completion of the line north of 42nd Street was pushed back to 1983 and the portion to the south in 1988.

[64] Of this failure to complete construction, Gene Russianoff, an advocate for subway riders since 1981, stated: "It's the most famous thing that's never been built in New York City, so everyone is skeptical and rightly so.

[75] The final plan called for the full-length Second Avenue line to carry two services: the T, with a route emblem colored turquoise,[2] as well as a rerouted Q train.

[101] Due to cost increases, several features of the subway were cut back soon after construction started: for instance, the 72nd Street station was downsized.

[128] The ceremonial first train, with several prominent officials in attendance, ran on New Year's Eve,[129][130] and regular service began at noon the next day.

[150] By August 2017, preliminary work on the line was underway,[146]: 48 [151] and design of the project was being performed by Phase 2 Partnership, a joint venture of Parsons-Brinckerhoff and STV.

[159][160] The MTA stated it would reduce the cost of Phase 2 by at least $1 billion through methods such as constructing smaller stations and platforms while also reutilizing tunnels built in the 1970s rather than demolishing them.

[165][166] Phase 4, which also has no funding commitments,[164] will provide an extension from Houston Street to a permanent terminus, with storage tracks, at Hanover Square.

[19]: 16  The Hanover Square terminal is only planned to be able to turn back 26 trains per hour instead of 30 as less capacity will be needed on the line south of 63rd Street.

[19]: 26  The Hanover Square station will be deep enough to allow for the potential extension of Second Avenue Subway service to Brooklyn through a new tunnel under the East River.

[171] Stations constructed as part of Phase 2 may receive platform screen doors depending on the results of studies being conducted for their installation elsewhere.

The tunnels near the 125th Street station would need to go through soft soil in addition to diving underneath the existing IRT Lexington Avenue Line.

[145]: 55–60 The Flushing Line station might have to be significantly reconstructed in anticipation of the increased volume of passengers and due to Americans with Disabilities Access requirements for the transfer.

[20][176] This option would require digging up Sara Delano Roosevelt Park to the east as Chrystie Street is not wide enough to fit four tracks.

In order to allow for sufficient room for stairways to transfer to the Second Avenue Line, the Grand Street station would be widened to have twenty foot wide platforms.

The tracks would be built at a depth of about 110 feet (34 m) under Water Street, allowing the line to be deep enough to tunnel under the East River for a possible future extension into Brooklyn.

[181] The rest of the cost, $800 million, was spent on "construction management, real estate, station artwork, fare-collection systems and other sundry items.

The Second Avenue Subway stations have full-length mezzanines, like the original IND but unlike other deep-level projects such as London's Elizabeth line.