What's confusing about R.I.P.? I honestly don't see it.
The Black Glove run by the evil Dr. Hurt has struck at Batman using a code phrase implanted by Dr. Hurt years ago, Zur-Enn-Arrh to zap his mind. They then drugged Batman and dropped him in the ghetto of the city to wander around amnesiatic and hallucinating.
Meanwhile, the Black Glove has moved into the Batcave, captured Alfred, captured Nightwing and imprisoned him in Arkham, and are going after Robin. And, rather than giving up, Bruce Wayne discovers there's a primal Batman deep within him and reinvents his identity.
That's the whole plot summarized in two paragraphs covering three issues. What's confusing about it? Yeah, we don't know Dr. Hurt's motivations and origins or what happened to Jezebel Jet, but there are three parts to go and is there any doubt that that information will be explained?
People seem to think that references and imagery to wild 50s stories are important plot points instead of thematic and symbolic points. Batman reinvents himself in his amnesiatic fugue state triggered by the phrase Zur-Enn-Arrh is linked to Batman constantly reinventing himself over the years, not to the Batman of Planet X being behind things. Bat-Mite is a psychological construct representing the pure, good, fun, and childish aspects of Batman, contrasted with a demon behind Bat-Mite in the previous appearance in Morrison's run. Don't people understand symbolism any more? Or how hallucinations can illuminate a character? Taking every image as literal reality and important plot points is missing the forest for the trees. Other than Tony Daniel's art being a little unclear in spots, I think people really underestimate how straightforward this story is. As far as I can tell, the only story of that era that you really need to know is "Robin Dies at Dawn" which Morrison himself explained earlier in his run.