Board Thread:General Discussion/@comment-26408694-20141004142023/@comment-24986099-20141004194216

I believe that Garnet is a fusion gem and that is the reason why she has two gems.

That aside; It's entirely possible that the blue gem is just a mechanism that allows access to the inner chambers and is not directly associated with a living Gem, as we have already seen that Gems are used to power devices.