The limits of what you can achieve with Construct 2 are up to you. What you describe is perfectly possible, maybe you will be the first around here to make a strongly story driven platformer. Go on, do it, and when you're done, tell us about it, I personally would be happy to play your game.
"can you make the game be a pop up window?"
This is not something you do in construct 2, you need to use the javascript function "open" or something similar.
http://www.w3schools.com/jsref/met_win_open.asp
Construct 2 exports the game as an HTML5 web page, you can do to your game anything that can be done to a normal website using php, asp.net, html, javascript and css. Of course you need to know a little bit about web development, there are plenty of tutorials for that, just google it.