The scenario is simple. Apple used patents that Motorola owns without paying for them. Apple will now be held liable until reasonable licensing fees are settled. And until that (or until an appeal) - Apple can't engage in certain commerce in Germany.
Or Apple will just cancel selling those products in Germany instead of paying Motorola. iPad 3 will be released in couple months and iPhone 4S isn't effected, so it might be cheaper than paying Motorola to cancel sales of those old products.