Like...

why were people frozen and put on ice cubes? What happened to them?
Who was it that got sent to kamandi's world?

Is batman in Earth-Zero's past? On an alternate Earth? KAMANDI supposed was supposed to be on the last page, wasn't he? And is everything still on New Earth or is that dead now?

And so many more...

Here's one summary I read. Hope it helps:

Darkseid tried to break New Earth. He succeeded, but in the process got himself nearly killed by the combined forces of Batman and the Flash.

In response, Superman had the rest of the survivors build the Miracle Machine to help rebuild the world, and stored the survivors in a frozen bottle city like state. (I think during this period is when Last Will and Testament has to happen.) He then finished off Darkseid's with his song, so Superman could rebuild the world with the Miracle Machine.

Mandrakk attacks now. When he arrives, Superman activates the Miracle Machine to make one wish (for a happy ending.) Cue the arrival of Nix Utuon from the Monitors with the help of god's army, an army of Supermen from the multiverse (collected by the Question after some of Checkmate was ported to safety on Earth 50), and the Green Lanterns. They attack and then the combined forces rebuild New Earth.

Finally, Batman is on Earth 51, sent somehow as part of a time capsule in that rocket in the first page.

morrison. sigh

Things I would add:

-Darkseid brought earth (and most of existence) into a singularity where "all was Darkseid." As Superman & Co. build the Miracle Machine, more and more of reality is washed away until, visually, we're left with only Superman, the Machine, and Metron's Chair. Basically, the void, where things pass on from the Multiverse. We know from SB #2 that Mandrakk wound up in the void. When he attempts to take his revenge on Superman, that's when the wish is made, and Superman powers the machine with his own energy.

-I've seen commenters say - and this isn't 100% clear - that the "hand" we saw at the beginning of time back in Crisis on Infinite Earths was Superman's powering the Miracle Machine to remake the world.

-The Monitors disappear. One of the last shots is Nix Uotan waking up back on earth. The Prime Monitor and Nix both stated that for the multiverse to survive and the Orrery to remain safe, the Monitors had to pass on.

So, per that suggestion, Morrison wrote Superman as God. Creepy man-crush ftl!

Hm. Thanks guys, that clears things up a little bit. I don't quite get why the monitors had to go (or even what was up with them being vampires)

@v: the best explanation I've seen for them being vampires is that the Ur-Monitor consciousness that contained the "flaw" of the multiverse sent part of itself to explore the flaw. The part that was sent (the original Monitor from COIE, who was Dax Novu, who became Mandrakk) grew, changed, and fed upon experience and the idea of Story. Since the "lifesblood" of any comic universe is Story, that is what the Bleed IS. So, them feeding on Story = them feeding on Bleed = them feeding on the life of the multiverse = cosmic vampires.

One interesting corollary to this is that the Monitors can only "feed" on and consume Story; they can't process it or make it new. That's because they're inherently reactive, and not part of the story themselves. Superman, since he's a character IN the story (and, by extension, the hand of the writer/creator), CAN use Story/Bleed for things.