On the eve of the trip, vandals attacked five churches with firebombs in the Chilean capital of Santiago and warned in a leaflet that "the next bombs will be in your cassock." That was an unprecedented threat against the pope and a violent start to what were already expected to be the first-ever protests against Francis on a foreign trip.
The Vatican agreed to the Chile visit knowing that the local church had lost much of the moral authority it earned during the Pinochet dictatorship, when bishops spoke out against human rights abuses when other institutions were silenced. But now, the Catholic Church in Chile has been largely marginalized, criticized as out-of-touch with today's secular youth and discredited by its botched handling of a notorious pedophile priest.
In Peru, Francis had hoped to highlight the need to protect the vast Amazon and its native peoples. But he now has to contend with a president who only narrowly escaped impeachment a few weeks ago, sparked massive protests by issuing a politically-charged pardon and is embroiled in a continentwide corruption scandal.
Here are things to look for in Francis' Jan. 15-21 trip, his 22nd overall and sixth to his home continent.
THE POPE AND INDIGENOUS PEOPLE
History's first Latin American pope will meet with indigenous groups in both Chile and Peru, evidence of his longstanding commitment to supporting native Americans in their struggles against poverty, discrimination and the exploitation of their lands.
The Chilean stop is more delicate: Francis will celebrate Mass for the Mapuche in southern Araucania on Wednesday and then break bread with a dozen or so indigenous at a private lunch.
But the visit comes as some radical Mapuche groups have been staging violent protests, occupying and burning farms, churches and lumber trucks to demand the return of their land. Protests are planned in Temuco during Francis' visit, and pamphlets left Friday outside the burned churches in Santiago exhorted the Mapuche cause.
Chile's largest indigenous group resisted conquest for 300 years, until military defeats in the late 19th century forced them into Araucania. Many Mapuche there now live in poverty on the borders of timber company land or ranches owned by the descendants of the Europeans who colonized the area after the indigenous resistance was quelled.
THE POPE, MIGRANTS AND THE POOR
Francis, whose defense of refugees and migrants is well-known, is expected to address Chile's growing immigrant community when he travels Thursday to the northern city of Iquique, home to nearly two dozen migrant slums. Even though its numbers are comparatively small, Chile had the fastest annual rate of migrant growth of any country in Latin American in 2010-2015, according to U.N. and church statistics.
Most of the newcomers are Haitians. While Chile isn't experiencing the anti-immigrant backlash seen in the U.S. and Europe, the incoming right-wing government of President Sebastian Pinera is looking to crack down.
In Peru, Francis will also visit Trujillo and the northern areas hard hit by floods and mudslides last March in the worst environmental calamity to strike Peru in nearly two decades. The El Nino storms killed more than 100 people and destroyed bridges, infrastructure and homes in hundreds of villages in an already poor area.
Peru's president estimates it will take $9 billion for the country to rebuild within five years.
CHILE'S SEX ABUSE SCANDAL
Chile's church has yet to recover its credibility following the scandal over the Rev. Fernando Karadima, a charismatic preacher who had a huge following in Santiago and was responsible for training hundreds of priests and five bishops.
The Vatican in 2011 sentenced Karadima to a lifetime of "penance and prayer" after confirming what his victims had been saying for years but what Chile's Catholic leadership refused to believe: that Karadima had sexually abused them.
Francis reopened the wounds of the scandal when in 2015 he named one of Karadima's proteges as bishop of the southern diocese of Osorno. Karadima's victims say Bishop Juan Barros knew about the abuse but did nothing, a charge Barros denies.
Osorno dissidents are planning protests in Santiago to coincide with Francis' arrival Monday.
POLITICS AND CORRUPTION IN PERU
Francis frequently rails against corruption, calling it more insidious than sin and a plague that harms the poorest the most.
But if he utters the word "corruption" in Peru, it will have particular significance. Last month, President Pedro Pablo Kuczynski narrowly avoided impeachment after an investigative committee revealed documents showing the Brazilian construction giant responsible for Latin America's biggest corruption scandal, Odebrecht, made $782,000 in payments to Kuczynski's private consulting firm more than a decade ago when he was a minister.
The former CEO of Odebrecht has admitted that company executives paid bribes and campaign contributions to secure public works contracts around the continent.
Soon after he survived the impeachment vote, Kuczynski set off protests by pardoning jailed former President Alberto Fujimori. Many Peruvians believe the pardon was done to secure support during the impeachment vote from a political party led by Fujimori's son.
THE POPE AND THE AMAZON
When Francis flies deep into the Peruvian rainforest to meet with indigenous peoples at the end of his trip, he'll be symbolically opening a major church meeting on the Amazon that is scheduled to start in October 2019.
Francis has called the Synod on the Amazon to bring bishops and cardinals from around the world to the Vatican to propose new ways to minister to Amazonian people and care for the "lung" of the Earth.
The area around Puerto Maldonado, at the confluence of two rivers on Peru's southern border with Bolivia, has the greatest biodiversity in Peru's Amazon, but is also home to a logging and gold-mining industry.
In his landmark 2015 encyclical "Praise Be," the pope railed against the exploitation of the world's natural resources by wealthy multinationals at the expense of the poor and indigenous peoples who need those resources to survive.
The archbishop of Lima, Cardinal Juan Luis Cipriani, said he expected the pope might speak out about the use of child labor in Peru's gold mines, the largest in South America, particularly when he visits a home for exploited children. Just last week Francis urged governments to prioritize the elimination of child labor "in all its forms."
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