On February 12, 2005, Sister Dorothy Stang, a Catholic nun and environmental and social activist, was gunned down in the Brazilian rainforest in which she had lived and worked for over 30 years. The trials of the gunmen and the rancher accused of arranging for her murder sent shockwaves through the environmental community, exposing the politics surrouding the battle over the future of the rain forest and the plight of the peasant farmers who live there. Stang, who was born in Dayton, Ohio, but became a naturalized Brazilian citizen, had fought and worked on behalf of the farmers of the region for decades, working with the Brazilian government to establish sustainable living communities that would allow poor farmers to survive while preserving the natural habitat from excessive deforestation.

Filmmaker Daniel Junge followed Stang's brother David to Brazil, to make They Killed Sister Dorothy, a documentary about Stang's lifework and the effort to bring her killers to justice. The filmmakers also had unprecedented access to the defendants and the defense team, allowing them to show both sides of the story. Sister Dorothy's perspective is told largely through interviews with those who knew her best: the peasant farmers among whom she lived and work, her fellow Sisters of Notre Dame, who lived and worked with her in Brazil, the federal prosecutor who was her friend and ally, and Sister Dorothy herself, through archival footage.

While those with whom she worked most closely viewed Sister Dorothy as an angel, to the loggers and ranchers who sought to clear the rainforest for logging and cattle enterprises, she was a "devil" who interfered with their plans, causing trouble and dissent. At the heart of the issue was a ten-square mile zone in the midst of the sustainable living project she was working on. The area was part of a region designated by the government for the project, but a wealthy rancher claimed to own it, putting him in direct conflict with Sister Dorothy as she fought to protect the forest, while he fought for his right to clear the land.

The lead defense attorney, Americo Leal, comes across as the quintessential bad guy; he repeatedly badmouths Sister Dorothy, attempting to portray her as a rabble-rousing radical, and accusing her of supplying high-caliber weapons to peasants and orchestrating murders herself. Sister Dorothy's supporters clearly found his premise laughable, and apparently the juries did as well, convicting the gunmen, who confessed to the crime (and repeatedly changed their story about whether they were promised money to murder the nun), the alleged middleman, and the rancher, Vitalmiro Bastos Moura. Leal does his game best to deflect the perception of his clients as bad guys, as he attempts to convince the jury that, rather than merely a case about the murder of a nun, it's really about North Americans coming into Brazil to stir up trouble and dissent. He even goes so far, at one point, as to accuse Sister Dorothy of being an agent of the US Government, deliberately sent to Brazil to cause conflict and further US interests there.

From a filmmaking standpoint, the film is well-shot, with the rain forest portrayed as much as a symbol of Sister Dorothy's work as for its own magnificence. Editing is mostly tight throughout, carrying the viewer along the narrative arc of what happened, and showing multiple points of view without being confusing.The filmmakers do a solid job of presenting the history of Sister Dorothy's life and work in the Amazonian rain forest and showing both sides of the conflict, but, like most documentaries, this isn't a purely objective film. It's clear from the outset on which side of the controversy around Sister Dorothy's death the filmmakers' sentiments lie. They Killed Sister Dorothy isn't just a film about a nun thwarting the attempts of honest ranchers to simply make a living; at its heart, this is really a story about the wealthy versus the poor, and about an activist trying to protect a natural resource from those who would destroy it for profit.

Sister Dorothy refused to leave her life and work in Brazil in spite of numerous death threats leading up to her murder; her brother, David, says in the film that he feels she knew she was going to be killed, and was willing to make that sacrifice to further her cause. In the wake of her death, the Brazilian government stepped up its efforts to carry through the sustainable living projects she fought so hard for; those communities, and this film about her life and death, will live on as her legacy.