A story about conquest, religion and the Americas, central to a founding myth of California, will end this year with the pope bestowing sainthood on a man many see as guilty of “ slavery ” and “ violent evangelism ”.

Pope Francis announced last week that he plans to canonize Junipero Serra, “the evangelizer of west in the United States” in a ceremony in Washington this fall, officially making the 18th-century missionary a saint.

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But many of the people descended from those who first encountered Serra have a starkly different view of the Spanish friar, whose proselytizing conveniently dovetailed with the less than Christian interests of the Spanish crown. Sainthood for the friar would honor the actions of a brutal colonizer, many Native Americans protest.

Ron Andrade, executive director of the Los Angeles City/County Native American Indian Commission, compared Serra to Hitler and the Spanish conquistadors who subjugated South America. Andrade, a Luiseño, said Serra “decimated 90% of the Indian population.” “Why doesn’t the pope canonize Pizarro or Cortez? It’s dumb.”

“Everywhere they put a mission the majority of Indians are gone,” Andrade said, “and Serra knew what they were doing: they were taking the land, taking the crops, he knew the soldiers were raping women, and he turned his head.”

Many tribes survived, including the Luiseños, Juaneño and Gabrielino-Tongva, survived the mission era through partial integration with each other and Spanish culture, but others fled inland or lost their culture completely, Andrade said.

“Serra was not the face of evil”, says Deborah Miranda, a professor of literature at Washington & Lee University and a Ohlone Costanoan Esselen Indian. “But there were so man atrocities happening and he closed his eyes,” she said.“I don’t think he should be rewarded for that.”

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For Miranda, Serra’s complicity in his fellows’ crimes outweighs whatever intentions he had or the inevitability of colonization. He was driven by ambition, she said, and in his desire to produce results for Spain he “laid the groundwork to erase our cultures and impose this burden of shame on Indians about being Indian.”

Serra came to the American territories in 1749 as an accomplished Franciscan, and after two decades of mission work the Spanish crown sent him with an army excursion to found settlements along the Pacific coast – before the Russians or British were able. In 1769 he founded the Mission of San Diego, the first of nine missions and traveled as far north as the San Francisco Bay.

Those missions irrevocably altered life for the people along the coast, whom Serra tried to convert as the army built fortresses nearby. “It was a very difficult time for California Indians,” says professor Steven Hackel of the University of California, Riverside and the author of Junipero Serra: California’s Founding Father.

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“They went to missions because they had few other options,” he said, since diseases devastated the tribes and the invasive plants and animals brought by the Spanish for agriculture overwhelmed native food sources.

Missions appeared to be “a place for them to rebuild their communities”, Hackel said, but as populations grew they became “disease factories”, as Miranda put it. Historians estimate that hundreds of thousands of Native Americans died in the decades after Europeans arrived, mostly killed by diseases.

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Converts were taught to farm, breed livestock and live in regimented communities utterly alien from their lives of hunting and foraging. They were flogged for disobedience, captured if they tried to flee, and sometimes raped by soldiers of the local garrisons.

French explorer Jean Francois de Galaup de la Pérouse, Serra’s contemporary, wrote that the missions treated “too much a child, too much a slave, too little a man” and were akin to slave plantations. On several occasions tribes tried to revolt, until eventually new settlers took over the missions.

“Serra didn’t believe you could beat Catholicism into an Indian,” Hackel said, “but he saw them as children, and in the early modern period good fathers corrected their kids through corporeal punishment.

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“I’m not trying to let Serra off the hook, but we need to understand how he understood the world.” Hackel said no matter what, “the Catholic church needs to do more work” to hear Native Americans’ concerns.

David McLaughlin, historian and executive director of the California Missions Resources Center, said that Serra should be said as a talented but flawed man of his time. He “lived an exemplary religious life by the terms of his day”, McLaughlin said, and the missions could be perceived as a“modification” that tried to reform the strategies that had devastated central American and Peru.

Father Tom Elewaut, a priest at San Buenaventura Mission – the last of Serra’s missions – defended the friar against criticism while acknowledging that colonization “was a tragedy” for its consequences. “Serra was a protectorate of the Native Americans,” Elewaut argued, saying that the friar never intended the spread of disease and cared deeply for Native Americans.

Serra prevented yet more garrisons from springing up near missions, McLaughlin and Elewaut noted, saying that he effectively guarded Native Americans from soldiers even if he had political considerations to do so.

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“Times change,” was Elewaut’s ultimate defense of Serra, “we had corporeal punishment in schools when I was a child, and it wasn’t devastating.” But Serra was “very respectful” to Native Americans who refused to convert, Elewaut protested, though he admitted the church should try to reconcile Native Americans’ “real hurt”. Elewaut said the best thing for the church and Native people may be to embrace Serra’s own motto: “‘siempre adelante, nunca atras’ – always forward, never back”.

For Miranda and others, the consequences of Serra’s brand of colonialism live on today. “Treating Indians as less than human, or as children who could never grow up, created a sort of psychological trauma,” she said. “I don’t deny that cultures evolve, but more agency in the evolution could not have been bad.”

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