The R160 order was to replace all R42s in the late 2000s, but 50 cars of the original fleet remained, when it was decided to retire the NYCT R44s instead.

After retirement, most of the R42s were sunk as artificial reefs, scrapped, or placed into storage, but a handful have been preserved and others retained for various purposes.

They were the first fleet of New York City Subway cars to be fully equipped with Stone-Safety 10 ton air conditioning systems/units.

[4] In 1973, cars 4764–4765 were sent to Garrett AiResearch's facilities in Los Angeles, California, to test out an experimental flywheel energy storage and energy-saving system and equipment.

Baloney coiled spring type inter car safety barriers were also installed on the blind ends of the married pairs.

[6] Morrison–Knudsen also removed the blue door indicator lights at the ends of the cars, but kept the original Westinghouse XM829 master controllers in their cabs.

On November 6, 2007, an M train of R42s was involved in an accident when the motorman attempted to relay it south of the Chambers Street station.

As the R42 fleet was being retired at the time, the entire consist[9] was hauled to the 207th Street Yard for reefing instead of being repaired, even though only the first two cars suffered major damage.

All of the Coney Island-rebuilt cars were retired first from July 2007 to May 2008 due to various structural and braking issues that plagued them throughout their rebuilt lifespan.

These 50 cars periodically underwent SMS (Scheduled Maintenance Service, a life extension program) cycles.

After the reefing program ended in April 2010, leftover retired R42s were trucked to Sims Metal Management's Newark facility to be scrapped and processed in mid-2013.