I've only scanned through the paper, but here's a rough summary of how it all hangs together.
From page 86 of the paper.
... polynomial time algorithms succeed by successively “breaking up” the problem into smaller subproblems that are joined to each other through conditional independence. Consequently, polynomial time algorithms cannot solve problems in regimes where blocks whose order is the same as the underlying problem instance require simultaneous resolution.
Other parts of the paper show that certain NP problems can not be broken up in this manner. Thus NP/= P
Much of the paper is spent defining conditional independence and proving these two points.