[3] He was appointed as Associate Commander of Hyesan (혜산첨사; 惠山僉使) due to the increased invasion of the Jurchens in the north but was unable to defeat them because of his disease.
In 1597, when the Japanese second invasion broke out, he was appointed as the Naval Commander of Right Gyeongsang Province to replace Bae Seol who fled from the Battle of Chilcheollyang.
After the Japanese Invasion of Korea, Chen Lin, a general of the Ming dynasty, recommended Yi as the Naval Generalissimo of the Three Provinces (삼도수군통제사; 三道水軍統制使), and although the Border Defense Council (비변사; 備邊司) agreed, Censorate (대간; 臺諫) opposed it.
[6] In January 1599, he resigned from his position as a Naval Commander and was appointed to the Police Chief (포도대장; 捕盜大將), but was dismissed for killing an innocent person.
In 1604, he was appointed the Fifth Minister (of the Office of Ministers-without-Portfolio) (첨지중추부사; 僉知中樞府事) and listed as the third rank of Seonmu Merit Subjects (선무공신; 宣武功臣) in recognition of his contribution during the Japanese Invasion of Korea in and given the title of Wansangun (완산군; 完山君).