The instructions explain how to combine the cards with the base game. I won't post the full information until VPG chooses to release the instructions, but basically, 1) you cannot use them with the tutorial (and you wouldn't want to!), 2) you can combine them with the classic version and campaign scenarios, and 3) they provide the neat card-flowchart for each of the campaign scenarios incorporating which cards are mandatory and which are randomized.
The expansion doesn't tell a different story; it's similar to the small set expansions for Arkham Horror -- it gets combined with the base game because it is not a stand-alone game -- adding in a few additional rules, counters and cards (2 extra heroes, extra civilians, extra Super Zeds, and about 25 each Event and Fate cards).
They've released the rules already. The funny thing is that they've given you just as many Fate cards as in the base game, which suggests that maybe you could just play with the new deck (new storyline).