Invoke javascript methods on a page
If you look at the HTTP request header you can determine the user-agent making the request.  Based upon that information you can write logic from the server side as to respond with a unique page per detected user-agent string.  Then you add any unique JavaScript you want as a static string to be executed by the user-agent application.
Is there a way using either C# or a scripting language, such as Python, to load up a website in the user's default webbrowser and continue to interact it via code (e.g. invoke existing Javascript methods)? When using WinForms, you can host a Webbrowser control and invoke scripts from there, but only IE is supported. Is there a way of doing the same thing in the user's default browser (not necessarily using WinForms)?
Update: The website is stored on the user's machine, not served from a third party server. It is a help page which works dynamically with my C# program. When the user interacts with my C# program, I want to be able to execute the Javascript methods on the website.