The baseband chip is a separate chip than the one providing wifi, bluetooth, nfc, etc. Essentially, the wifi/bt/etc chips fall on the computer side and can be controlled/manipulated by the phone's OS. The baseband chip is a standalone system that is controlled by the cell towers, and then is tied into the phone's cpu directly. Phone builders essentially buy the baseband chip that is certified on different network types and add it to their PCB.

In reality, the baseband should be connected more like a serial port (with some audio channels to the mic and speaker). In fact, it's treated very much that way in software - you interact with it by sending AT commands. But, as others have pointed out, it can send commands directly to the phone's CPU and access the phone's internal memory.

Interested in the answer to this question.