This question has been posted before but I did not see anything in those posted solutions doing something about the standalone ASPX pages which can be created through SharePoint Designer
The thing about the standalone ASPX pages is that they are not connected to any SharePoint master page so is there any way to make the JavaScript appear in these standalone pages?
Instead of regular pages which will have something like this in the page directive right at the top
<%@ Page language="C#" MasterPageFile="~masterurl/default.master" %>
in standalone pages you will see the MasterPageFile attribute will be missing
Reference Links-
Add Javascript to every page in Sharepoint 2013
How to not use SharePoint master page
I am interested in solutions that work for SharePoint 2013