This example may be doing what you want.
It loads scene one.
When the button is clicked it loads scene one into the iframe.
There is a scene load action to check to see if the loading window is the top window <- source for top window idea.
If it is not the top window then we load scene2 instantly. This will only load scene 2 in the iframe.
It is not perfect and will need a lot of finessing but I think it is what you are talking about.
Since we need to load the foo.html file in the iframe, I have set it up so it can be tested with preview or when exported without you having to change anything.
I do think though that it would be easier to have each scene a separate documents and load those as needed.
You would be able to do it similar to what I have done here by setting the source.
innerIframe.hypetemplate.zip (26.7 KB)
But I may still not fully understand.
If I am completely wrong in my understanding of you goal (suspect I am) then please do look at this thread which is similar to what I was referring to in my original post