The Pope travelled to the far eastern Philippines to comfort survivors of the devastating Typhoon Haiyan, then cut his own trip short because of another approaching storm.
After a windy and rainy morning mass, Pope Francis headed to an abbreviated lunch with 30 survivors of the 2013 storm, and then to a cathedral in the city of Palo.
Entering without the usual ceremony and procession, Pope Francis took the microphone and told a surprised crowd that he would have to leave four hours ahead of schedule.
"I apologise to all of you," he said, speaking in Italian through a translator. "I am sad about this, truly saddened."
The Pope said the pilots of the Philippine Airlines jet told him the weather would worsen, adding: "We barely have time to get to the plane."
Some of the priests and nuns in the cathedral groaned, though mostly in a good-humoured way.
The Pope's plane apparently left without incident but a private jet carrying several Philippine cabinet officials who accompanied Pope Francis to Leyte blew its front tyres during take-off following the Pope's plane and veered off the runway.
There were no injuries and ambulances evacuated the passengers, police said.
Earlier, Pope Francis had addressed 150,000 Catholic faithful gathered in an open field near the airport in Tacloban, the city hit hardest by Typhoon Haiyan.
He told them: "So many of you have lost everything. I don't know what to say to you, but the Lord does know what to say to you. Some of you lost part of your families. All I can do is keep silent. And I walk with you all with my silent heart."
Many in the crowd wept as Pope Francis spoke, overcome by the memory of the November 2013 storm that levelled entire villages with ferocious winds and 21ft waves and left more than 7,300 people dead or missing. The Pope joined them in solidarity, even donning the same yellow rain poncho over his vestments that mass-goers were given because of the rain.
Tropical Storm Mekkhala was expected to make landfall on nearby Samar Island in the late afternoon or early evening with winds of 60mph-80mph, the weather bureau said.
Pope Francis drew applause when he told the audience that he had decided to visit the city of 200,000 in 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."
Pope Francis spoke in his native Spanish, which he reverts to when he wants to speak from the heart. He ditched his prepared homily and instead composed a brief prayer off the cuff that began: "Thank you, Lord, for sharing our pain. Thank you, Lord, for giving us hope."
As he spoke, the winds whipped the altar cloth and threatened to topple the candlesticks.
After the mass, his motorcade took him past cheering crowds
After a quick exchange of gifts, in which Pope Francis received a wood image of Our Lady of Immaculate Conception made from the debris from the typhoon-damaged church, his motorcade sped to the airport in Tacloban.
The papal delegation was soaked when it boarded the plane, and trip organisers asked the flight crew to turn off the air conditioning to prevent the passengers from catching a cold.
Ferry services were suspended to Leyte province, stranding thousands of travellers including some who wanted to see the Pope.
A police official estimated the crowd at the mass at 150,000 before the Pope's arrival and said tens of thousands more were lined up outside the airport area.
Pope Francis blew kisses, waved and flashed the thumbs-up sign to the crowd while riding on a covered popemobile from the airport terminal to the nearby altar.
Pope Francis is in the Philippines after stopping in Sri Lanka earlier in the week.
Tomorrow, he is due to celebrate the final mass of the visit in Manila's Rizal Park, where as many as six million people are expected. St John Paul II drew a record five million people to his final mass in Manila in 1995, and organisers say they think Pope Francis could top that record.