About 850 customers were on board the disabled train, and the passengers were transferred to a rescue train and taken back to the 23rd Street-Ely Avenue station in Queens.
E, F and M service was restored with delays.
The incident caused a backup and massive delays, as trains stuck behind the disabled train had to reverse course and head back to Queens as well.
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The MTA is waiting for the delays to resolve themselves.
As a result, southbound E trains were running on the F line from Jackson Heights-Roosevelt Avenue to West Fourth Street-Washington Square.
Metropolitan Avenue-bound M trains were running on the F line from 36th Street in Queens to 47-50 Streets-Rockefeller Center. Some Metropolitan Avenue-bound M trains were running via the J line from Essex Street and then terminated at Chambers Street.
The E, F, M and J trains were all impacted, and riders were advised to allow additional travel time.