What's the significance of what happens to Simon at the end of Chapter Nine? Why did that happen to Simon?
As always when you look at specific chapters and their importance you need to examine their significance in the context of the whole book. This chapter symbolises the end of any vestiges of civilisation on the island and in the community of the boys. At this stage Jack and his hunters are nothing but inhuman savages filled with bloodlust and able to commit heinous crimes with a clear conscience. Ralph's followers at this stage become depressed and consider joining Jack and his gang, and all are involved in the ritual dance around the fire following the murder. In a highly significant piece of pathetic fallacy, the storm that rages over the island after Simon's death symbolises the chaos and anarchy that have overtaken the island and the boys and also reminds us of the catastrophe of the murder and what it represents.
In a sense, after Simon's confrontation with the Lord of the Flies, where the Lord of the Flies promises that he will have some "fun" with Simon and Simon realises that the beast is actually within us all, it was clear that Simon would need to confront the beast in the other boys. The Christ-like parallels between Simon and Jesus are maintained here (though not completely), for Jesus and Simon are both killed for the truth they possess. However, unlike Christ, Simon is not given a chance to share his truth. Also, of course, the function of the deaths are very different: Jesus died to save mankind, whereas Simon's death only serves to highlight the moral degeneracy at the heart of man and ushers in even further oppression and darkness in the novel.