NOAA Ship McArthur II was built by the Tacoma Boatbuilding Company in Tacoma, Washington. After the ship was acquired from the U.S. Navy, the ship was commissioned on May 20, 2003, and was converted by NOAA from a T-AGOS surveillance ship to a multiple-disciplinary platform capable of a broad range of missions. Like its predecessor, NOAA Ship McArthur, McArthur II was named after William Pope McArthur. The ship was homeported at NOAA's Marine Operations Center—Pacific in Newport, Oregon.

The ship conducted oceanographic research and assessments throughout the eastern Pacific, including the U.S. West Coast, Central and South America. McArthur II was involved in studies in several of the National Marine Sanctuaries on the west coast of the United States. The 224-foot ship measured chemical, meteorological, and biological samples for several large scale programs within NOAA.