In brief, unscripted comments, Francis took the microphone soon after arriving at the main cathedral in Leyte province and told a surprised crowd that he would have to leave at 1 pm, four hours ahead of schedule.
"I apologize to all of you," he said, speaking in Italian through a translator. "I am sad about this, truly saddened, because I had something prepared especially for you."
Some of the priests, nuns and others in the cathedral groaned, though mostly in a good-humored way.
Francis traveled to the far eastern Philippines to comfort survivors of the devastating 2013 typhoon, himself braving rains and heavy winds from an approaching storm and conceding that it was hard to find the right words when surrounded by so much pain.
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Tropical Storm Mekkhala, packing winds of 100 kilometers (62 miles) per hour, suspended ferry services to Leyte and stranded thousands of travelers including some who wanted to see the pope. With the winds strong enough to blow away thatched roofs common in the regions, it is forecast to slam ashore on nearby Samar Island later today.
Many in the crowd wept as Francis spoke, overcome by the memory of the Nov. 8, 2013, storm that leveled entire villages with ferocious winds and 7-meter (21-foot) waves and left more than 7,300 people dead or missing.
He drew applause when he told them that he had decided to visit the city of 200,000 in the eastern Leyte province in the days immediately after the storm.
"I wanted to come to be with you. It's a bit late, I have to say, but I am here.