What is the relationship between MCU and NOISII core?

I downloaded the gateware project , when I opened it with QuartusII, found there were some NOISII source code.
when I compiled the FPGA logic and NOISII code together to combine a programmable file.if I use the file to program FPGA, when powering up the board, do I need to program the MCU with another MCU programming file ? how about the relationship between NoisII and MCU, how about the MCU source code and MCU source code?