In 1986, the IND practice of using double letters to indicate local service was discontinued. The CC service was renamed the H.
In 1988, the K train was discontinued, and the C train was extended to run at all times except late nights. It ran local to Euclid Avenue midday and rush hours (the A ran express in Brooklyn during this time), and to World Trade Center during evenings and weekends.
On March 1, 1998, the B and C trains switched northern terminals, with C terminating at 168th Street.
Starting in 1999, C trains ran local to Euclid Avenue and A trains ran express in Brooklyn at all times except late nights.
On January 23, 2005, a fire at the Chambers Street signal room crippled A and C service. Initial assessments suggested that it would take several years to restore normal service, but the damaged equipment was replaced with available spare parts, and normal service resumed on April 21.