travelling through (or arriving "in") the heart of a bad or dangerous area in the context of having no other alternative, such as on the front lines of a war, or in the general area of the war-torn area. In another similar context, one could think of it to mean being in the most dangerous and critical of situations, such as being a cop working undercover infiltrating a mob
family -- being in that crucual position of having gained the mob's trust and being a key part of its operations, would be considered being "in the belly of the beast."
JJ is going undercover, it could be dangerous. He's in the belly of the beast.