You can keep the PDF on the server location and create a Virtual Directory for the same. And you can create handler that fetches the pdf URL from server and returns URL to server.
Suppose you need to fetch PDF based on object id of feature and your handler is WebHandler.ashx.
1. Use dojo.xhrPost to make a call to Handler.
2. If PDF is stored with object id then just append the ObjectId to URL of PDF folder or write your logic in handler to fetch the PDF based on objectId/ or some other field.
3. Return the url from handler and catch the result in xhrPOST.
With the use of handle you can also end the response and prompt the user with download dialog by setting the Response header and ending the response.
Vinay Bansal