I have a C# code that works perfectly when compiled in visual studio. However it contains some .NET code that is not supported by MONO framework. If I add this code as a plugin to Unity, will it work?
Also what is the difference between adding a dll of that file to the working folder instead of pluging it in?
A .Net DLL isn't the same as a normal native code library. Your .Net DLL is a big pile of .Net opcodes and is expecting certain libraries to be available in your GAC (Global Assembly Cache).
Long answer long... no, the DLL will not work if it requires things that are available in .Net but not in Unity's version of Mono. If you really wanna try your hacking hand at things, you can copy your referenced .Net assemblies into the Mono.framework that's in your Unity install.
it will not work. plugins must be mono supported assemblies or native code libraries. the only way to use .net is to write c++ dlls that use .net as a com component or interupt with .net code themselves.