Denis Johnson, who has written poetry, reportage, plays, and a substantial body of fiction about addicts, drifters, prostitutes, and thugs, is one of our poets of the deeply damaged. His portraits of men and women slipping from the lower rungs of society, notably in “Angels” (1983) and “Jesus’ Son” (1992), are so unpatronizing and fully realized that they suggest a personal familiarity with life among the lost. His best work takes on the characteristics of a lucid dream — not a Hollywood nightmare, but the kind that leaves you with a disturbing unease you cannot explain. As in dream life, the bizarre and extreme register as unquestionably true, almost unremarkable, and trauma blooms without warning into beauty.

“Tree of Smoke,” Mr. Johnson’s first full-length novel since the publication 10 years ago of “Already Dead,” is a sprawling epic of more than 600 pages, with an ensemble cast of major characters. They are generally more cerebral and in higher places than the types he usually spends his time with, but they share the habit of getting themselves in deeper than they should. The novel is about the Vietnam War and its legacy of ruined bodies and even more wrecked minds, and it surely represents a huge investment on Mr. Johnson’s part of blood, sweat, and years. The book is full of incident and rat-a-tat dialogue, and is peopled by undercover operatives; soldiers in action; agents who might be double agents; desperate aid workers; and friends, family, and lovers who often act as if they are nothing of the sort. There is movie potential here, but a film would never be able to capture the richness of interior life that is Mr. Johnson’s greatest achievement.

Colonel Francis X. Sands, the most memorable character, endured a Japanese prisoner-of-war camp in World War II and has cut a path through the psychological operations division of the CIA, devising unconventional ways to manipulate the enemy mind. A theorizer who enjoys dispensing wisdom with a heavy hand, he’s a titanic drinker and a tough guy with a formidable intellect and unbreakable confidence. He’s also very funny. “Talk to my ass,” he’s fond of saying. “My head aches.” A catalyst in the military and intelligence community who likes to color outside the lines, he is invariably called “the colonel.”

The point of view in “Tree of Smoke” is an effective hybrid of third-person omniscient and third-person limited; each section provides the convincingly complex thoughts of only one person, but this focal character keeps shifting, sometimes within a page, and more than a handful of people get a substantial portion of the book. Often we badly want to know what someone else is thinking, but Mr. Johnson either denies us entirely or elegantly builds tension by withholding this knowledge. Both the characters and the reader are only fractionally aware of need-to-know information, and, to borrow from Defense Secretary Rumsfeld, the unknown unknowns loom large. The rooms of the novel are never lit by a switch, but with a flashlight pointed at one corner at a time.

William “Skip” Sands, whose slice of the book is the largest, is the colonel’s nephew and a junior CIA agent in PsyOps. He lost his father in the attack on Pearl Harbor, but has found in his uncle a mentor and a fellow believer in the American cause. Skip’s intellectual development, gradually and intricately charted by Mr. Johnson, comes about through the outsize influence of the colonel but also through a genuine curiosity about foreign countries and firsthand experience with a deception that cuts both ways.

Skip’s first substantial assignment, arranged by the colonel, involves gathering intelligence on a priest suspected of running guns to Muslim guerrillas in a rural area of the Philippines. There Skip meets a nurse working for an NGO, Kathy Jones, whose missionary husband has just been killed. Together they begin a fraught love affair, and they both end up in 1967 in Saigon, where Kathy’s religious faith is set against a despair that renders her increasingly brittle. As the priest, marooned in the jungle, declares, “Here, of course, where the people are so poor, so sick, you can’t love them. … Everyone here knows how to love, but love them back — it’s quicksand.” The Philippines mission ends with a planned but senseless murder magnificently realized by the author. So begins Skip’s acquaintance with futility and a creeping, bewildering betrayal that forces him to make serious compromises with himself.

Skip clings to the colonel’s view that PsyOps has a broad definition and entails becoming familiar with the foundations of enemy thought. “War is ninety percent myth, isn’t it?” the colonel says:

In order to prosecute our wars we raise them to the level of human sacrifice, don’t we, and we constantly invoke our God. It’s got to be about something bigger than dying, or we’d all turn deserter. … I think we need to be invoking the other fellow’s gods, too.

To that end, the colonel has Skip manage voluminous intelligence files on the local Vietnamese. It’s a fool’s errand, but the intelligence gathering lends itself to a wide-ranging and painterly portrait of Vietnam as seen through Skip’s eyes. The country’s poverty and casual cruelty both repel and fascinate him, and Mr. Johnson does not shy away from conveying the grim desperation of the place and the ugly thoughts Skip and others cannot suppress. We get luminous descriptions of the sky and the suffering spread widely beneath it, and Mr. Johnson skillfully and consistently evokes the appalling appeal of war:

Around them beggars and urchins crawled at the feet of exiles and campaigners — at last, a wartime capital, a posh lobby full of sagas, busy with spies and cheats, people cut loose and no longer accountable to their former selves. … This was what he wanted.

Skip’s pursuit of cultural understanding is part of the colonel’s grand, unauthorized plan. The operation involves cultivating a Viet Cong double agent — himself an artfully depicted central player — to bring a momentous piece of disinformation to the North, with the aim of planting a new American myth, a “tree of smoke” meant to billow all the way to Uncle Ho: “To hell with reason, categories, synthesis, common sense,” Skip thinks. “All was ideology and imagery and conjuring. Fire to light the minds and heat the acts of men.” The colonel dearly wants to win — indeed, his certainties outlast almost everyone’s — but the peril that closes around him and his protégé comes from those on their own side. The loyalties here and everywhere in Mr. Johnson’s Vietnam are tenuous, and the terms of all contracts are subject to change without notice.

Interwoven with this high-wire plot is the ground-level story of Bill and James Houston, poorly educated sons of a single mother in Phoenix who sign up for the military underage. The brothers each cross paths with the colonel, but the men giving orders that determine their fates are never clearly in their sight lines. Bill, a sailor in the Navy, shoots a monkey in the Philippines in the opening scene, the day after the Kennedy assassination, “without really thinking about anything at all,” and cries when it dies in his arms. His recklessness keeps getting him demoted, until he is cut loose back to the Arizona desert, where the qualities need in war are no longer of use.

James joins the Army, leaving a girlfriend behind without regret, and after a lot of drinking and misbehaving finds himself in an exhilarating and terrifying combat episode during the Tet offensive. His devil-may-care bravery takes him further in the military than Bill, which only gives him farther to fall. Mr. Johnson writes boldly, to the point that the way the brothers and a few others discuss big ideas and emotions occasionally strikes a false note. But while James repeatedly professes stupidity and he and Bill can’t seem to do the right thing, the author still makes it impossible to look down on them — one of Mr. Johnson’s trademark strengths.

Even when we realize these plotlines are leading nowhere good, the sense of foreboding does not diminish the pleasure of watching it all unfold. The colonel’s mysterious exit from the book occurs out of sight, which is liable to disappoint, yet is consistent with his place in the picture — he is not just a man but an also the embodiment of an idea that leads those around him to various hearts of darkness.

The parallel stories progress from 1963 to 1970 — the early stages of the American involvement — through a final chapter set in 1983, and they convey a full-blooded sense of the personal force of history. Mr. Johnson’s narrative of an improbably ambitious mission guided by an increasingly embattled raison d’être will be mined for comment on today’s war in Iraq. But at bottom this is not a political novel. War may be 90% myth, but it is 100% real to those it touches and breaks, and their lives are at the vivid center of Mr. Johnson’s canvas. Vietnam and Iraq are only two nations “where theories burned to cinders,” as Mr. Johnson writes, “where questions of morality became matters of fact.” With its humane depiction of the most private battles within battles, “Tree of Smoke” ought to take its place among the great American novels of any war.

Mr. Hughes has written for the New York Review of Books, the New York Times, and the Boston Globe.