The epigraph is a verse from the Gospel of John, chapter 12, verse 24: unless a grain of wheat falls into the earth and dies, it remains alone; but if it dies, it bears much fruit. It comes before the preface, without commentary, and the book returns to it twice.
The first return is in Book VI, on the last afternoon of Elder Zosima. He tells Alyosha to seek out Mitya, says that he prostrated himself before Mitya's great future suffering and, without explaining, has the disciple keep the verse. The second is in the account of Zosima's life: when the mysterious visitor hesitates to confess a crime of fourteen years earlier, Zosima shows him the same verse.
The sense the book gives is that of a loss that bears fruit: the suffering that awaits Mitya, the death of the elder, the visitor's chosen pain, the boy Ilyusha, who asked to be buried beside the stone and was buried in the churchyard enclosure. None of these cases is explained by the verse; all of them can be read with it. It is up to the reader to decide whether there is fruit.
It is worth reading the epigraph as the summary of a wager. Ivan's thesis, that of the child who suffers without compensation, calls for a response that is not an argument; Zosima's is that nothing bears fruit without passing through loss, and the book does not prove it, only shows it on stage.