In the winter of 638-639 virulent plague broke out in Syria, Egypt and Iraq. The plague exacted its heaviest toll in Syria, particularly Amwas, and the plague came to be known as the Amwas plague.
When Umar heard of the outbreak of plague he decided to proceed to Syria personally to watch the measures to be adopted to suppress the epidemic.
When Umar reached Surgh a few stages from Madina, he met Abu Ubaida and other officers of the Muslim army in Syria. He was told that the virulence of the plague was increasing and that people were dying in thousands.
Many persons advised Umar that he should not proceed to the infected area. Umar held a counsel. Abu Ubaida suggested that Umar should visit the infected areas. Abdur Rahman bin Auf quoted a tradition of the Holy Prophet according to which the Holy Prophet had enjoined that when plague was raging one should not go from the non-infected to infected area or vice versa. That settled the issue and Umar decided to return to Madina.
Abu Ubaida did not feel happy at the decision of Umar. He said:
"O Amir-ul-Mumnin, why are you flying from God's will." Umar replied that he merely moved from one will of God to another will.
On return to Madina, Umar addressed a letter to Abu Ubaida asking him to come to Madina as he wanted to consult him on some important matters. Abu Ubaida guessed the purpose of the call and wrote back saying that Fate ruled everythtng, and that he could not move away from Syria to save his own life leaving others in danger.
Umar thereupon asked him to move the troops to a healthier place. Abu Ubaida accordingly moved the troops to Jabiah which was noted for its good climate. A few days after the arrival of the troops at Jabia, Abu Ubaida caught plague and died. Before death he appointed Muadh b. Jabal as his successor.
Some Muslims held that the plague was a calamity. Addressing the troops on the occasion of the Friday prayer, Muadh said that the plague was not a calamity; it was a mercy of God. The son of Muadh caught plague. While his son lay on his death bed, Muadh addressing him said, "My son this is a visitation from God. Let there be no doubt in your heart on this account." The boy said, "You will find me resigned to the will of God" and with these words he breathed his last.
When Muadh returned after burying his son, he fell a prey to plague, and died a few days later. Amr bin Al-Aas succeeded him as the Commander-in-Chief of the Muslim forces in Syria. Amr bin Al-Aas shifted the troops to the hills. This measure proved satisfactory, and plague no longer menaced the troops.
When the fury of the plague was over, leaving Ali in charge of Madina, Umar travelled to Syria accompanied by his slave Yarfa. He first went to Ella in Palestine. A story is told that at Ella, he gave his shirt to the local priest to have it mended. The priest had the shirt mended. He also presented a new shirt to Umar, but he did not accept the gift.
From Ella he proceeded to Damascus. He disbursed the salaries of the troops personally. Calling for the heirs of those who had died in the plague, he put them in possession of their inheritance. He established military outposts at strategic points and had the fortifications strengthened.