Set largely in modern-day Johannesburg, Jongo tells the origin story of a young man who has an array of supernatural abilities after an alien crystal is found in a cave at the Cradle of Humankind. The stone is left to him by his father, an enslaved miner who was murdered shortly after escaping from the cave. As Eli tries to deal with the death of his father and sets out to find the men responsible, he must also grapple with the powers of the crystal and how it will indelibly alter the course of his life. What Eli doesn't know is that the men he is hunting have crystals of their own and need Eli's stone to fulfil an ancient prophecy which will threaten the lives of millions. Caught up in the middle of everything is Maya, the love of Eli's life.