There is nothing like client side or server side. It is the environment where the code is being executed. In your server you have a container that is interpreting you C# code and compiling it to machine instructions. But in your web-browser there is some one to interpret your js code, that is know as javascript compiler like V8 in google chrome.
So if you have any C# sharp code that has some Javascript code too... Its C3 part will run in the server and output a code containing HTML, JS and CSS. So this is the servers output after applying the business logic.. the output code will run on Browser and since browser is intelligent enough to understand the HTML , Javascript code.
So this way your C# and Javascript code will execute.