If your documents are stored in SharePoint and these have to be referred in an external application, considering that users dint have access to SharePoint, you can program to get the file form SharePoint and put it to the browser from the external application.

You can get file contents (media resource) by file name:

<<site url>>/_api/Web/GetFileByServerRelativeUrl(‘<<Server Relative URL of File>>’)/$value

Below is a C# sample on how to get the file content

private void CallRestApi()
{
try
{
HttpWebRequest endpointRequest = (HttpWebRequest)HttpWebRequest.Create(<<REST URL>>);

endpointRequest.Method = “GET”;
endpointRequest.Accept =” application/json;odata=verbose”;

string username = “<<user name>>”;
string password = “<<password>>”;
string domain = “<<domain>>”;

NetworkCredential cred = new System.Net.NetworkCredential(username, password, domain);
endpointRequest.Credentials = cred;

byte[] byteArrayUP = Encoding.UTF8.GetBytes(username + “:” + password);
endpointRequest.Headers.Add(“Authorization”, “Bearer” + byteArrayUP);

HttpWebResponse webRes = (HttpWebResponse)endpointRequest.GetResponse();
txtResponseHead.Text = webRes.Headers.ToString();
Stream output = webRes.GetResponseStream();
using (var fs = new FileStream(“<<path to file>>”, FileMode.OpenOrCreate))
output.CopyTo(fs);
}
catch { }
}

Reference URL: https://msdn.microsoft.com/en-us/library/office/dn450841.aspx