Gagnon founded the Cutivereni mission in Peru's Ene River valley to assist the indigenous Asháninka people who were being forced out of their homes in the jungle by settlers.

[2][3] Gagnon's fascination with Peru and the Asháninka began after World War II, when he heard a bishop give a talk about them.

"[4] He also observed that they did not chew coca leaves and were not prone to sharing food and drink, which had been a major cause of rampant tuberculosis.

He maintained the Cutivereni (alternate spelling Cutivireni) mission of the Ene River parish in the Peruvian Amazon, southeast of Satipo.

The mission was equipped with a plaza, a chapel, a generator building, an infirmary, a bilingual school, workshops, and a landing strip.

Although taught modern technology and facilitated Spanish lessons with the Summer Linguistics Institute, a Protestant organization, for the indigenous people, he did not try to change aspects of their culture, like polygamy or women going topless.

As the trade grew in the area, though, Gagnon talked to a United States Drug Enforcement Administration agent and sent a letter to the Peruvian security police base commander in Mazamari in 1983.

[2][5] The Franciscans who were working with the Asháninka did not have a coordinated strategy to provide for their defense, but Gagnon was able to secure weapons from the Peruvian army, and approached the United States military for support as well.

Two mission leaders and two schoolteachers were killed by the guerillas, and a war broke out between the people at Cutivireni and the Shining Path fighters.

[2] In April 1990, he arranged for several hundred Asháninka to make a five-day trek from the central highlands into the mountains of Peru at Tzibokiroato.

[a] During this time period, he was recalled by his religious superiors to Lima, where they questioned his arming the Asháninka, because of the view that the Catholic Church should not use violence.

[2][7] In September 1990, the village that they had built of houses in the remote location was surrounded and attacked by guerillas of the Shining Path while Gagnon was in Lima strategizing with others on ways to protect the indigenous people from being killed, enslaved, or indoctrinated.

[13] Anthony Wilson, OFM said, "Many referred to Mariano as a modern-day hero for his work during the time of terrorism in the Peruvian Amazon.