When we compile our .NET code then it is not directly converted to native/binary code; it is first converted into intermediate code known as MSIL code which is then interpreted by the CLR. MSIL is independent of hardware and the operating system. Cross language relationships are possible since MSIL is the same for all .NET languages. MSIL is further converted into native code.
When the Web Service (or Web Forms page) is implicitly compiled, it is actually compiled twice. On the first pass, it is compiled into IL. On the second pass, the Web Service (now an assembly in IL) is compiled into machine language. This process is called Just-In-Time JIT compilation because it does not occur until the assembly is on the target machine.