When Harry Kim came to his rescue in 2377, he asked Kim to pilot the ship, since the captain and his officers had been killed in a battle with the Annari. He deceived Kim into helping him by pretending to be a doctor who was transporting vaccines to his people.
Kim found out later that Loken was not a doctor, but a scientist who was developing cloaking devices for the Kraylor fleet. Kim did deliver the ship back to Kraylor, but did not feel good about his first command. (VOY: "Nightingale")