This question doesn't make alot of sense honestly. You may have a misconception about how this all works together.
The c# code is running on the web server, and the output is Html code that is rendered down to the browser, including javascript.
The Javascript is loaded into the browser and executed locally on the client's computer.
If your trying to manipulate or control some aspect of the client page load with javascript or something either add the script to the page itself (.aspx file) register and stream it with Client.Register api calls, or add a < script .... > tag to import it into the file.
I have no idea what Web.cs class is doing, I would assume its some kind of logic or business object. You'll need to communicate the need for the client script from it back to the presentation layer to get it to run client side.
If you are somehow under the impression that you can run javascript from the server side, you are mistaken.
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