At the start of the American Civil War, Wells was suffering from exhaustion and exposure from this travels, coupled with depression from the recent death of his beloved brother-in-law, with whom he had sailed for twelve years. Consequently, he spent three months in the Pennsylvania Hospital for the Insane in Philadelphia where he was diagnosed as having Melancholia, being released on October 11, 1861, to return to active duty. He was appointed executive officer of the and took part in the capture of Port Royal, South Carolina, on November 7, 1861.