I would not recommend 1980s neo realist perspective to be applied to a post 9/11 phenomenon. Neorealism was severely criticized during the post cold war years owing to its inability to predict the end of cold war despite its claims to scientific accuracy. Having said this, if you would like use this lens to understand war on terror , you may focus on anarchic nature of international structure , US ability to take a unilateral stance, to bypass UN on this issue can be highlighted. Imbalance of power distribution in the world, unipolarity of world order may also be discussed at length.
Also, if you want to use realism, and explain the middle east might I suggest 'Internal Balancing' or 'omni-balancing' borrowing from Hanz Morgenthau's earlier work 'Politics Among Nations'.
For an intro/ cursory perspective, this is a great book with many cited scholarly works you can then consult if needed...and has a section that focuses on Pakistan: https://books.google.ca/books?hl=en&lr=&id=OOGTyh675JYC&oi=fnd&pg=PR7&dq=intra+balancing+middle+east&ots=i6eivcekov&sig=Ao3oqFc6pj1fvvBYwo5HW9Arfk8#v=onepage&q=intra%20balancing%20middle%20east&f=false.
Dear Fatima, Neorealism, and IR theory more generally, has been roundly criticized for failing to take into account religious passions in international relations. A thorough response from neorealism is Jack Snyder's recent book on Religion in IR Theory. Theoretically, what the War on Terror has done to political science, is to turn to Comparative Politics for insights in the War on Terror. THis is a good development.
Thank you Timothy Lomperis , I agree , Jack Snyders' book is an interesting read , it provides useful insights to someone examining War on terror from neo realist / IR theory perspective. But for someone like me having post modern, post structural , post colonial orientation , theorizing / generalizing world politics becomes problematic. I would say what War on terror (or rather the failure of it )has done to political science is to give way to alternative / non American way of doing Political Science/IR . Why should we have to 'apply' certain theoretical lens proposed by someone from a different world to understand our own world ??
Refer the book written by J.J. Mearsheimer, "The Tragedy of Great Power Politics" and Scott Burchill book Theories of International Relation. Hope you will get some ideas.