Johnson’s story is peppered with many characters, whose personalities and histories range from the benevolent to the bizarre, but there are four main figures in Tree of Smoke: Colonel Francis Sands, Skip Sands, William Houston, and James Houston.

Much of the novel revolves around Colonel Francis Sands, a legendary figure who works for a special intelligence branch of the armed forces. He was once a teacher of military strategy and has many admirers as well as detractors. Some believe the Colonel is a traitor, running his own branch of the military, and they are astonished by how easily he can create his own base of operations without any orders from headquarters. Others are in awe of him and believe in all his theoretical ideas on how to win the war in Vietnam. Colonel Sands wants to outwit Ho Chi Minh, the leader of the enemy in North Vietnam, by using psychology rather than military power. What the Colonel ultimately plans to do, however, must be kept secret, even from his commanders.

Skip Sands is the Colonel’s student and his nephew. Skip lost his father in the Japanese attack on Pearl Harbor when he was a very young boy. The Colonel became a father figure to Skip. Throughout the novel, Skip, who works for the CIA, is often accused of being a traitor to his uncle, and it is never quite made clear if this is true. Skip works pretty much on his own, similar to how his uncle operates.

The Houston brothers, William and James, might be called the lost boys of this novel. They have no father figure, and their mother is absorbed in religion and offers them no sense of security. The brothers have separate experiences in the war, but both come home completely broken psychologically. Both are discharged with less than perfect records, and both have serious problems adjusting to life back home. They typify Vietnam veterans who never recovered from the war.