When it comes time to compile the new kernal, the compiler loads both the original Linux kernal source, and the Microsoft patches, combining them in internal memory, and compiles the resulting program, automatically. This compiled product is special in another way; it compiles the Linux kernal as normal, binary indistinguishable from a kernal running on any other system, but produces a shell-kernal that wraps the Linux kernal and adds the hooks into the system that Microsoft wants added.