Special to the AmNews

July 29, 2012, in Aguelhok, a small city in northern Mali, more than half of which was being occupied by men who were outsiders, an unspeakable crime took place to which the media largely turned a blind eye. A young couple, blessed with two children, were stoned to death.

Their crime? They weren’t married. The video of their killing, which was posted online by the perpetrators, is horrid. The woman dies, struck by the first stone, as the man lets out a hollow rasp of a cry. Then silence. Soon after they were buried, they were dug up to be buried farther away.

Filmmaker Abderrahmane Sissako’s bold film, “Timbuktu,” is masterful storytelling from the first frame to the last, leaving a lingering impression of deeply felt human emotion that is presented in richly shaded tones.

Sissako sets the story in the earliest days of the jihadist takeover of northern Mali in 2012, where intolerance and swift condemnation walked hand-in-hand. Yet, under this director’s skillful eye, the story never succumbs to creating plastic perpetrators. There are levels of empathy for both sides in the complicated lives of a people living in a complicated land.

In a nod to Greek chorus structure, Sissako cleverly conveys the multicultural makeup of the area, where city dwellers of various ethnicities and the nomadic Tuareg people coexist in generally respectful fashion.

The film is partly an immigrant story of newly arrived Arabic-, French- and English-speaking jihadists who methodically patrol the city and its environs (the actual shooting was done in the Mauritanian cities of Oualata and Nema). The no-tolerance zone was enforced with bans on soccer, music, most socializing and uncovered women. The local imam (Adel Mahmoud Cherif) calmly tries to argue against their narrow, ultra-orthodox dogma, but his influence is flimsy and fleeting.

The neat trick is that there is no stereotypical demonizing of the jihadist captains. Instead, there is outward sympathy as the community attempts to hold to the very strict interpretation of their scripture.

One of the best moments that displays this balance is when Abdelkrim (Abel Jafri) drives to the tent of a Tuareg family to convince the strong-willed Satima (Toulou Kiki) to cover her head. Her smarter neighbors have, wisely, already fled, and she tells her loving husband, Kidane (Ibrahim Ahmed), that they should move closer to other people, but he wants to stay put.

A tinderbox is ignited by a simple, childish mistake. Kidane, a goat and cattle herder, is the father of Toya (Layla Walet Mohamed), 12, and guardian of orphan Issan (Mehdi AG Mohamed). While driving the herd to water, Issan loses control of the animals, and a prize cow gets caught in the nets of fisherman Amadou.

The innocent mistake escalates, and a furious Amadou spears the beast. When Kidane arrives, he displays his pistol purely as a visual threat, but a physical struggle causes the gun to discharge and the fisherman is killed.

This incident leads to a swift punishment, not only for Kidane but also for others who have transgressed the fundamentalists’ interpretation of Sharia law.

In town, soldiers unleash their simmering anger and arrest four people for making music, subjecting the singer Fatou (Fatoumata Diawara) to 40 lashes. She kneels, dressed in a black abaya, tears staining her face, gently crying out and softly singing.

The landscape is almost a character in the story, and its simple beauty is an eerie background to mounting anger that will eventually lead to bloodshed.

Individuality is being extinguished, and Zabou (Kettly Noel), a “colorful and harmless madwoman,” is on the self-designated Islamic police radar to be shut down.

“Timbuktu” gives solid insight into the root of the intolerance that wasn’t grown from Malian soil, even if the relationship between nomadic shepherd and rooted fisherman is fraught with its own tension. “We are the guardians of all deeds,” says a jihadist to the imam, thereby dismissing any attempt at freedom of expression and movement.

Every performance is mesmerizing, even the smallest roles. Sissako uses color like a renaissance painter unleashed, and she holds the eye without distracting from the story. Cinematographer Sofiane El Fani’s work has never been finer. The music is a combination of traditional Malian melodies and more Western orchestral accompaniment. Everything matches beautifully.

“Timbuktu” opens Wednesday, Jan. 28 at Film Forum.