If you view the page source in your browser for your ASP.NET app, you will see all the generated .axd (javascript resource files) that ASP.NET creates on the fly.
As Raynos said, Javascript is run on the client machine and ASP.NET runs on the server.
ASP.NET requires the use of the client-side Javascript, as that's how ASP.NET handles its Events via PostBacks. Like I said though, this is the auto-generated Javscript that is done for you on-the-fly in temporary external .axd files.
Now, on top of the auto-generated Javascript, you can make your own Javscript methods that lessen the need for Http Requests / Round Trips / PostBacks. You could create and include a foo.js file and put whatever functionality you want to handle there. Or, you could just put your Javascript inline with your HTML by putting it inside of <script type="javascript"></script> tags. Also, you can move server-side functionality to the client by the use of page methods, which basically creates a Javascript function out of your server-side method and allows you to use it client-side.
Personally, I like to use a Javascript framework called, jQuery for my client-side needs. I suggest googling some of the above and see what fits best for you.