Is there a reason it should be externally?
Why not use what you have at your disposal inside Construct2?
Because I need to call external js to show ads and their js needs to control if game should be paused or not. Thats how it needed to be done - Ive managed.
I just had to hack my code inside of prototype.logic function with simple boolean that optionally skips whole logic loop. Added 2 window functions - stopGame and resumeGame they are basically available everywhere as "cr_..." function is called in index.html.
Only disadvantage is that i will have to edit my c2runtime everytime I make adjustment for client but it only takes 1 minute so I can live with that.