The problem is, for one, a supply issue. Dry weather in West Africa (specifically in the Ivory Coast and Ghana, where more than 70 percent of the world's cocoa is produced) has greatly decreased production in the region. A nasty fungal disease known as frosty pod hasn't helped either. The International Cocoa Organization estimates it has wiped out between 30 percent and 40 percent of global coca production. Because of all this, cocoa farming has proven a particularly tough business, and many farmers have shifted to more profitable crops, like corn, as a result.
Then there's the world's insatiable appetite for chocolate. China's growing love for the stuff is of particular concern. The Chinese are buying more and more chocolate each year. Still, they only consume per capita about 5 percent of what the average Western European eats. There's also the rising popularity of dark chocolate, which contains a good deal more cocoa by volume than traditional chocolate bars (the average chocolate bar contains about 10 percent, while dark chocolate often contains upwards of 70 percent).
For these reasons, cocoa prices have climbed by more than 60 percent since 2012, when people started eating more chocolate than the world could produce.
The article doesn't account for the completely untapped Indian rural markets and the consumption is certainly on the rise. Here's another post comparing chocolate consumption in developed and emerging markets.