In January of 1895 a plaque of smallpox swept through Haifa. His landlady, Sister Hilt, warned him repeatedly not to go into the city, but Elder Clark felt the Lord would protect him and that he should go. He insisted, "I am not a child any more. I know what my mission is here." He seemed to feel driven to mingle with the people, as he was mastering Arabic and could now share the gospel. So he continued his daily routine. He came home one Wednesday evening, January 30, having caught the "black smallpox" and was sick for nine days. It was a dreadful disease with black blisters and high fevers. There was not much that the doctors could do to relieve his suffering. Because no one in Haifa other than John, could speak or write English, his landlady sent word to his parents, via Switzerland, that John was sick. They had isolated the house and prayed that he would recover. The first eight to fourteen days were the worst.

By the time his parents received word that John was ill, he had already been dead three weeks. He was buried eleven hours after he died-a bloated corpse. His bed and most of his belongings were burned to prevent the plague from spreading. Everyone in the house was under a six-week quarantine and friends shunned the house for fear of catching the dread disease. They buried John in a cemetery at the foot of Mount Caramel. He had been serving as a missionary for only about one year; although he planned to serve for three. He died on February 8, 1895.

His father wanted to ship the body home and made repeated trips to Salt Lake to make arrangements, but it was not allowed because of the plague. His mother cried in anguish to understand the purpose of the Lord taking her son. Her letters to John's landlady reflect her struggle to understand and accept the Lord's will.

“Will you please write and tell one all the particulars of his (John's) sickness and death and burial and what his last words were, weather