When the CFNR lease was terminated, the NCRA took over operations using "Black Widow" EMD GP9 and SD9 locomotives running both freight service and occasional passenger excursion service from Santa Rosa and Healdsburg to Willits from 1996 to 1998. The line was plagued by a series of harsh El Nino storms causing washouts and bridge instability until the FRA shut down all operations over the entire length of the line. The six Black Widows were returned to their lessor Omni-trax in 1998, and former SP SD9s, leased from BUGX, and former North Coast Railroad GP9s, owned by the NCRA, were pressed into service. These locomotives and some maintenance of way equipment remained in storage at the Willits and Schellville yards, with the first set being returned to BUGX in December 2016.