Following the 9 April 1940 German invasion of Norway, she was requisitioned by the Norwegian authorities and carried troops for the Norwegian war effort until the forces in Western Norway ceased fighting on 2 May 1940.
After a brief stint in German service, she returned to her civilian duties later in 1940,
She remained in service until 8 February 1945, when she ran aground in the Alverstraumen narrows. Kommandøren remained aground for five weeks, and was filled by sea water before being salvaged and towed to Bergen to await repairs. Although the ship’s hull was intact, the interior and engine were heavily water damaged.
During the night of 29 March 1945, Kommandøren was docked at the remains of Søndre Nykirkekai in Bergen. At around 01:00 the ship was struck by one of two torpedoes accidentally fired by a German torpedo boat anchored on the opposite side of Vågen bay. The torpedo explosion threw debris from Kommandøren over a wide area, and left the ship lying on the harbour bed. Only the mast and a section of the bow remained above water.The midship and aft sections of the ship were completely destroyed by the torpedo. The only crew member on board at the time, Able Seaman Alf Larsen, was killed in the incident.
Before discovering that the incident had been caused by the accidental launch of two torpedoes by a drunken German crewman on the E-boat S-13, the German authorities in Bergen launched a search for saboteurs in the city. Kommandøren was the only total loss suffered by Fylkesbaatane i Sogn og Fjordane (the formerly named Nordre Bergenhus Amts Dampskibe) during the Second World War.
- Most of the quay Søndre Nykirkekai had been destroyed in the 1944 Vågen explosion less than a year previously.