It was truncated in 2004 to its current service pattern, running local on the Broadway Line to Whitehall Street until June 25, 2010, when it was eliminated due to the Metropolitan Transportation Authority (MTA)'s financial crisis.

[12] The W label was first used in 2001, when the two tracks on the Manhattan Bridge's northern side, which connected to the IND Sixth Avenue Line, were closed for repairs.

The W also replicated the split in B service from 1986 to 1988, when the bridge's north tracks were first closed, although both halves of the route were labeled B.

[20] Service began operating between Coney Island and Astoria–Ditmars Boulevard, Queens, via the West End Local and Fourth Avenue Express in Brooklyn; the Manhattan Bridge south tracks; Broadway Express (switching to the local tracks to serve 49th Street) in Manhattan; and the 60th Street Tunnel and BMT Astoria Line in Queens.

The W ran express on the Astoria Line during weekday daytime hours in the peak direction between 6 a.m. and 9 p.m., and local at all other times.

[22] After September 11, 2001, all Broadway Line service in Lower Manhattan was suspended due to extensive damage caused by the collapse of the World Trade Center.

As a result, the entire N route was suspended, and W trains ran at all times between Ditmars Boulevard and Coney Island.

[26] On September 8, 2002, W service was extended to Astoria during late nights and weekends, running fully local via the Fourth Avenue and Broadway Lines and Montague Street Tunnel.

The W ceased operation on Friday, June 25, 2010, with the last train bound for Astoria–Ditmars Boulevard leaving Whitehall Street–South Ferry at 10:50 p.m.[36][37] In July 2015, the MTA announced it was considering restoring the W with its 2004–2010 service pattern following the opening of the first phase of the Second Avenue Subway, which would reroute the Q from the Astoria Line to 96th Street on Manhattan's Upper East Side.

The W's restoration meant there would be 20 fewer trips to and from Astoria per weekday as the W ran for a shorter time span each day than the Q did.

[44] As the N and W share the same fleet from the Coney Island Yard, a small number of W trains originate or terminate at 86th Street throughout the day.

[48] In their proposal, the MTA noted that service often ended early on weeknights to accommodate planned work.

[47] In March 2020, the W was temporarily suspended due to lack of ridership and train crew availability caused by the COVID-19 pandemic,[49][50] though full service was restored in June.