At the beginning of the play, Brutus Jones is an emperor on an uncharted island in the Caribbean (West Indies). Previously, Jones had killed a friend (Jeff) over a game of dice, was sent to prison, and then escaped from prison. He escaped to this island and established himself as emperor using his street smarts. Upon becoming emperor, Lem hired another to kill Jones. However, the gunman missed and Jones killed him instead. Jones told the locals that the gunman missed because he (Jones) had a magical charm and could only be killed by a silver bullet. This gave the locals the impression that Jones did have some sort of magical power; therefore, they initially feared him and he was thus able to sustain his position as emperor, albeit temporarily.
Eventually, the locals rebelled. Smithers clued Jones in on this and Jones gave up being emperor and attempted to escape through the forest. As he makes his getaway, he has hallucinations and flashbacks of his past. He sees an image or ghost ("ha'nt") of Jeff playing dice. He sees his fellow prisoners and the guard he knocked over in his escape. He also has hallucinations of being on a slave ship, a slave auction, and a Congo witch doctor. He has essentially traveled a trail of hallucinations back in time: from his own past to the past of his ancestors.
Over the course of Jones' life, he was certainly the victim of racism. But as he became emperor, he became racist against whites (Smithers) and even the black natives on the island. This is evident in how he speaks about them and how he rules over them as a greedy tyrant. "Think dese ig'nerent bush niggers that ain't got brains enuff to know deir own names even catch Brutus Jones?"
As Jones goes through the flashbacks and retreats to the past, Jones changes from confident emperor to a cowering man geographically and mentally lost. At the end, he is completely lost, literally going in circles, haunted by his own past sins and the complex, conflicting history of slavery. So, there is a lot more going on here than just a man running away. Jones revisits his past sins in flashbacks but also, in doing so, confronts the history of racism and slavery. Given his treatment of the locals on the island, he had turned his back on his ancestors; as emperor, he'd become more like the auctioneer than the slaves. This, in addition to killing Jeff, and fear for his own life all led to his disintegration and pleadings for mercy and forgiveness from God.