Here's what I think:
In Episode III, we will see arguments and such between Amidala and Anakin, possibly even more. Hiding her pregnancy from him is not hard as he is busy with Empire conquests, and such. She has the twins in secrecy, and in fear of Anakin's ever prevailing evil side, sends them off.
Anakin's outfit will resemble the Vader outfit with cape, armor. While he will not be completely corrupt and evil in the beginning of the movie, he is very close to being totally in the dark side. Throughout the movie, he will progress into the dark side realm until the final straw, which will be the duel between Obi-wan and Anakin. At this point, as described in the novelization, Anakin will fall into a pit of lava, and be scarred so horribly that only the Emperor's offer of the suit can save him. (in the novel, there is a pause in Obi-wan's description of the event. This could possibly be because just as he told Luke his father was dead, he later revealed the truth. Perhaps Anakin didn't fall, but was shoved by Obi-wan. He didn't want Luke to know). The movie will end not much further along by explaining a few things, and making some ties together.
Naturally, there will be other events taking place, but I feel this will be as the main plot with Vader.