Scene 6. It is now three o'clock in the forest, which now looks "like the dark, noisome hold of some ancient vessel. The moonlight is almost completely shut out and only a vague, wan light filters through." Jones enters, moaning. He worries about what he will do next, as he has only the silver bullet left in his gun, and needs to keep that one for luck.
A group of figures can suddenly be seen behind Jones, a group of black people, "naked save for loin cloths." They sway forward in unison, and the sway becomes more like "the long roll of a ship at sea." They begin to wail loudly, and Jones is filled with terror. He begins to wail with them, swaying back and forth and screaming with their same sorrow. As he does so, the other voices stop. As the forest darkens, Jones makes a run for it.
Scene 7. At five o'clock, we see the foot of a large tree next to a river, with an altar of boulders surrounding it. Jones enters and kneels before the altar. He suddenly becomes frightened, and asks God to protect him. Suddenly, the Congo witch-doctor appears next to the tree. O'Neill describes him as "wizened and old, naked except for the fur of some small animal tied about his waist, its bushy tail hanging down in front. His body is stained all over a bright red. Antelope horns are on each side of his head, branching upward. In one hand he carries a bone rattle, in the other a charm stick with a bunch of white cockatoo feathers tied to the end. A great number of glass beads and bone ornaments are about his neck, ears, wrists, and ankles."
Jones is afraid, and the witch-doctor begins to sway and dance, doing some kind of ritual, and trying to keep demons at bay. As "the forces of evil demand sacrifice," the witch-doctor points at Jones and decides that he must be sacrificed.
The witch-doctor goes to the river bank and a large crocodile comes onto the bank, and makes to attack Jones, but he pulls out his revolver and shoots the crocodile.
How far Jones has fallen from his elevated position at the beginning of the play. While he was a confident autocrat at the start, he now finds himself in dire straits, beset with horrible hallucinations, and violent dissenters nipping at his heels. Jones' descent into madness and complete desperation is reflected in his appearance; while he was dressed elegantly at the start of the play, he finds himself crawling around the forest in tatters by Scene 6, unsure of how he will make it to morning.
With every break he takes in his escape, Jones is visited by horrific visions of violence and trauma. In Scene 6, he faces a group of Africans on their way to be sold into slavery in the United States. They form a communal mass, swaying as if on a ship, and moaning and wailing about their plight. It is a fearsome image, and Jones must reckon with the post-traumatic hallucination head on, since he no longer has enough bullets in his gun to fight back. In this moment, he becomes merged with the vision, and it becomes an outlet for his own desperation, a layering of past on present that allows him to express his own abject terror.
The play follows a very set structure, and is essentially a monologue for one actor, at least in the middle. Jones wanders through the forest, attended by visions and hallucinations, but these projections only make his solitude more stark and dramatic. He speaks to himself, because none of the wooden, strange figures in his imaginings will interact with him. The forest plunges him into a solitude unlike any other, one that puts him in contact with the darkest reaches of his memory, both historical and personal.
In Scene 7, Jones goes back even farther into history, back to Africa, where even more mysterious and fearsome forces await. He is faced with the presence of a Congo witch-doctor, who decides that Jones must act as a human sacrifice to keep the evil forces at bay. Rather than kill him himself, the witch-doctor conjures a crocodile to emerge from the nearby river. The line between reality and fantasy has become completely blurred, and it is unclear if this crocodile is a hallucination or a real element in the treacherous forest.
Many have noted that O'Neill's play engages in a racist depiction of blackness. Try though it might to depict the horrors of white supremacy and the slave trade to show that Jones is a victim of a system that has devalued and abused him, Emperor Jones also represents blackness as akin to mindless savagery, and traffics in gross stereotypes—stereotypes that led the originator of the Brutus Jones role, Charles S. Gilpin, to have a falling out with Eugene O'Neill in the process. While the play addresses the ghosts of American racism and slavery in a way that is undoubtedly critical for the time in which it was produced, its depiction of Jones' travails seems to equate blackness with a hallucinatory and chaotic moral order.