The following version of this book was used to create the guide: Klay, Phil. Missionaries. Penguin, 2020.

Klay's novel is divided into four books, the first two in first-person perspective and the second two in third-person. Each one of the four narrators introduced in Books I and II will have some personal involvement in either or both of the historic Colombian civil conflict and the present and future conditions of the peace process. Book III converges the main characters' plot lines on the way to the novel's climax, providing partial resolution that is contextualized in Book IV's epilogue.

Book I begins with Abel, a boy in a remote war-torn region of Colombia, and tells his life story from his birth in 1986 to the murder of his parents by FARC guerrilla in 1999. When he was eight years old, the guerrilla appear to seek vengeance on the town for its betrayal and Abel's father hides him under a seat in their boat before being rounded up with the rest of Abel's family and locals, herded into Chepe's bar and then incinerated. While standing stunned at the smoking ruins, Abel is approached by some skinny boys with rifles who beat him unconscious, and transport him somewhere with a gasoline-soaked rag stuck in his mouth. When Abel revives, he is greeted tenderly by Osmin, then dumped bleeding on the side of the road. Abel lives the next two years like an animal on the streets of a larger neighboring town. One day in 2001, he sees Osmin again, who gives Abel the chance to join the local paramilitary, ostensibly to fight the guerrilla but primarily to extort and intimidate the locals through extreme violence and terror. Soon, the commander of the regional paramilitary factions, Jefferson comes to town and soon takes Abel under his wing, making the teenaged Abel his chief negotiator and civil project manager. With Uribe elected as president in 2002, the paramilitaries are disbanded and their combatants pardoned, while leaders like Jefferson receive just a two-year jail sentence for their crimes against the people in the government's name. Jefferson will stay in Venezuela after jail and build his drug connections, while Abel will stay in the town of La Vigia to learn how to live responsibly on his own.

Book I also introduces Lisette, a foreign-war correspondent from Western Pennsylvania on extended assignment in Kabul, Afghanistan in 2015 covering the ongoing American military involvement there. She explains that after fourteen years of war against the Taliban, the recent removal of regular U.S. combat troops has led to a resurgence of bombings targeting civilians. She had always thought of Afghanistan as the “good” American war in comparison to Iraq, because she believed the Americans were helping to accomplish something positive in Afghanistan by providing security for the civil society to strengthen. After a particularly trying day of four bombings around the city, injuring not just civilians but an American Special Forces commando, Lisette decides to go home to visit her mother and dying Uncle Carey after a long time away. Although Lisette loves her free-spirited, All-American, Vietnam-veteran uncle, he knows as well as she does that Lisette's place is fulfilling her vocation wherever the world calls her and that her mother is fine without her. She reaches out to her ex-paramour Diego, a former Special Forces operator in Afghanistan turned private military contractor now based in Colombia and on his suggestion, decides to go there.

Book II introduces the novel's other two narrators, Mason and Juan Pablo, both military men. In 2004-2005, Mason is a medic and a new addition to a Special Forces team in Iraq, tasked with training the Iraqi security forces while also arresting former Saddam Hussein loyalists now involved with the anti-American, anti-Shi'a insurgency. While Mason sees some effectiveness in the training mission, he soon begins doubting the counter-insurgency tactics that have painful unjust consequences for the children and families of the men they arrest, often deathly so. In 2006, Mason and his team are deployed on a non-combat training mission in Colombia, when he notices a kill-oriented mentality infecting the Special Forces, the army's corps of “warrior-diplomats” (99). In Afghanistan in 2007, Mason's reservations about his mission and his role as a new father cause him to reassess his priorities, especially after the death of an innocent child and old man after an excessive use of force by the ground troops. It becomes clear that the same tactics will only breed more resistance and instability.

Juan Pablo is introduced in Book II the evening of his family dinner with Sergeant Major Mason Baumer, Special Forces liaison with the American embassy in Bogota in June of 2016. Juan Pablo is a lieutenant colonel in the Colombian Special Forces in command of an operation that will assume military control of the regional anti-narcoterrorist campaigns, draining assets from the local police forces who would normally have jurisdiction. When his daughter Valencia is is invited to join her law professor on a volunteer project with a social justice foundation in La Vigia, Norte de Santander, Juan Pablo reluctantly gives her his blessing, but only after conducting an investigation into the region. He hears from a member of the Colombian national legislature who is the only representative from the district and she tells him about the regions' current threat, a former paramilitary boss turned narco named Jefferson. Were the military to escalate its involvement in the U.S.-sanctioned assassinations of drug lords and affiliates, it would be much worse for the region than the common tyranny of Jefferson's group, the Mil Jesuses.

Book III picks up in 2015-2016 with Jefferson's return to La Vigia and into Abel's life, pulling Abel back into service to Jefferson advance Jefferson's agenda and inform against the town. When Lisette arrives in Colombia, she begins background research on the story she plans to write about the positive results from the U.S-backed military efforts, and meets up with Diego to press him for some inside information. In turn, Diego reaches out to Mason, his former Special Forces teammate in Afghanistan, who directs her to Norte de Santander. Around the same time, the Colombian military has been using Abel as a mole in Jefferson's gang, providing useful intelligence and convincing him to plant a tracking device in a box of action DVDs to present to Jefferson. At a roadside checkpoint that appears a routine FARC shakedown, some untrained gunmen pull Lisette out of the van and beat her viciously, forcing the Colombian group to leave her behind. While Lisette is being treated at a nearby clinic, the beacon Abel helped to plant guides the military in pinpointing Jefferson's location and killing him in a sloppy version of a Hollywood shootout, after first killing Abel in the opening assault outside the house.

Book IV concludes the novel with Juan Pablo in the United Arab Emirates a few months after the peace vote, where he is working for a private military contractor identifying Houthi targets in Yemen for elimination by airstrike. His team contains people from around the world fighting this remote war in a critically underdeveloped desert nation, where despite the sophisticated weapons systems available to the “primitive” rebel extremists, famine and disease ravage the civilian population. Now that he does not serve the national military, Juan Pablo is content to earn a life-changing salary and apply his expertise where it is needed without political interference. Juan Pablo is unemotional about the civilian cost of war, but recognizes the need for the forces of civilization he represents to neutralize the threat of terror and extremists violence.