Twenty years ago, protesting the coming celebrations of the 400th anniversary of the first Spanish settlement in what is now the American West, operatives in a shadowy group called the Friends of Acoma took aim at the towering statue here honoring Oñate.

In the dead of night on Dec. 29, 1997, they sawed off the foot, unleashing a debate over Oñate’s atrocities. While some in New Mexico admire the conquistador in ballads and pageantry, others are re-examining the brutality of Oñate’s conquest.

Scholars have documented how Oñate oversaw atrocities that included the killing of 800 people in Acoma Pueblo, an ancient adobe aerie atop a 357-foot-tall sandstone mesa where the Acoma people still live today. Dozens of Acoma girls were parceled out to convents in Mexico City, and adolescents were sentenced to decades of servitude. In a notorious act of cruelty, Oñate is said to have ordered his men to cut a foot off at least 24 male captives.

Chris Eyre, a Cheyenne-Arapaho filmmaker who is well known in Santa Fe, said that the foot abductor recently walked up to him while he was at a local eatery, La Choza, digging into a bowl of posole. “He handed me a note, and I thought to myself, is this one of those Roswell types?” said Mr. Eyre, 48, referring to the conspiracy-minded U.F.O. trackers who convene in the New Mexico desert.

Still, Mr. Eyre, the director of “Skins,” a 2002 film that ends with a depiction of red paint being thrown on George Washington’s face at Mount Rushmore, was intrigued by the story of the foot. Now Mr. Eyre is developing a documentary exploring how the amputation triggered an exploration of New Mexico’s complex history.

“Trump asked if all this stops with Washington or Jefferson,” said Mr. Eyre, referring to the president’s comparison in August of removing statues to “changing history.” “For me, that’s actually where it starts because we need to go back a whole lot further to examine the crimes upon which these lands were claimed.”

Mr. Eyre arranged an encounter in September between this reporter and the thief, a wiry figure who trekked to the remote meeting point carrying his piece of Oñate. Chafing at celebrations of the Spanish conquest while describing his own Iroquois ancestry, the thief said he carried out the amputation in 1997 with just one comrade, a native New Mexican, in solidarity with the Acoma people.

He requested that their identities remain secret, explaining that he had no desire to go to jail. “Mysteries are sometimes best kept a little mysterious,” he said. “I smile at the possibility that this tale of defiance could someday be told from campfire to campfire.”