I just read Morrison's Batman RIP, Batman and Robin, and Return of Bruce Wayne in the space of a couple nights. That story makes SO much more sense when you read it all at once
One thing still confused me. When we see Darkseid and Metron in Return #6, was that just in Bruce's head and they weren't literally still alive? At once point Bruce says that Darkseid is trying to reincarnate in Doctor Hurt... but the Omega Sanction was going to destroy reality... they seem like contradictory plots, though I suppose a truly reincarnated Darkseid would survive the Omega Sanction destroying reality...?
So summarize... Bruce was infected with the "hyper-adapter" beast which was going to destroy the Earth when he got back to the present, but they managed to send the beast back in time to avoid this, where it infected Thomas Wayne in the 1700s, who became immortal and ended up Doctor Hurt. And the Omega radiation was dissipated by allowing Bruce to die for two minutes.
Also, Talia going nuts in Batman Inc works better for me now. I had forgotten the whole bit of her trying to control Damien, showing him the clone they're growing of him, and her swearing vengeance when he rejects her once and for all.