Military scientists and entomologists (basically bug scientists) have teamed up to discover that it's a combination of a fungus and a virus, a sort of kick ass one-two punch that knocks bees down for the count.
They're unsure how the combo works but it makes for a killer cocktail that does its damage in the bee's belly (leaving scientists to think it's nutritional). It's been known that the fungus was part of the problem, but new software developed by the military uncovered a new DNA-based virus called N. ceranae.
What's crazy is how these bees die:
One perverse twist of colony collapse that has compounded the difficulty of solving it is that the bees do not just die - they fly off in every direction from the hive, then die alone and dispersed.
Image via wherethebeesat