Is this closer to your intent?
AliReport_v1_JHSv1.hype.zip (1.1 MB)
Your design is engaging. But...
I've spent most of my time figuring out what You were requesting... while You did a good job in general of labeling your elements, some of them were generic - e.g. "Rectangle 1"; "Text 1"; etc. If You wish to access the expertise of this Forum everything You can do to make our understanding of your layout as easy as possible is a Beautiful Thing - so please label ALL your elements with descriptive names - You are far more likely to get help.
I do not have enough time to go into detail but your problems devolve into two main issues:
1) Elements were covering other elements (why the "Main Menu" did not work). "0" opacity does not mean the element disappears from influence. You need to set the "Display" property to "Hidden".
2) One element (the "Close" text button) was assigned to run one timeline - but You were expecting it to run two ("Mission" & "Foundation"). There are now two elements running these two timelines ("Close Foundation" & "Close Mission").
Separately - I've re-labeled the "generic" names of your provided project to descriptive names in my example. e.g. "Rectangle 2" is now "Foundation-Mission Cover Bg" as it covers the background of the Foundation~Mission statement with a solid black overlay. Season to your taste.