In 1943, the Navy asked for control of Sea Cloud and Nourmahal, another former yacht converted into a weather ship. On April 9, 1943, the United States Navy commissioned Sea Cloud as USS Sea Cloud (IX-99), though she maintained a Coast Guard crew.2 She was assigned to Task Force 24.
Relieving USCGC Conifer in February 1944, Sea Cloud patrolled a 100-square-mile (260 km2) area near the New England coast, generating weather reports for the First Naval District. On February 27, 1944, Sea Cloud traveled to be refurbished at Atlantic Yard in East Boston, afterwards taking over a new one-hundred square mile area at Weather Station Number One.2
On April 5, 1944, Sea Cloud received radar indication of a small target at position 39°27′N 62°30′W, bearing 350° at 3,000 yards (2,700 m).2 General quarters were sounded and battle stations manned, but contact was lost ten minutes later. The target was identified as a submarine, but after Sea Cloud carried out standard anti-submarine drills with no evidence of damage being inflicted, she returned to port.2
After minor repairs, Sea Cloud was rebased to Argentia, Newfoundland, where she was assigned to Weather Station Number Three. While patrolling the area on June 11, 1944, the crew spotted a Navy Grumman TBF Avenger, exchanging recognition signals. Sea Cloud received orders to report to the escort carrier Croatan and join the five other escort ships under her command. The envoy searched for a raft reported in the area, but returned with no sightings. After this event, Sea Cloud was once again reassigned to Weather Station Number Four. After a search for a downed aircraft, she returned to port in Boston. Sea Cloud was decommissioned on November 4, 1944, at the Bethlehem Steel Atlantic Yard and returned to Davies, along with $175,000 for conversion to pre-war appearance.2
For her wartime service, Sea Cloud was awarded the American Campaign Medal and the World War Two Victory Medal.