In 1999 she was extensively rebuilt, and then she was moved to the Anacortes–San Juan Islands route.[1] She was removed from service in the spring of 2014 to have her drive motors rebuilt, and returned to service in Fall 2014.
In March 2016 there was a fire on the vessel while running in the San Juan Islands. The vessel clogged passage to and from Friday harbor for several hours and the ship was out of service for some time. The Yakima has since returned to service in the San Juans.