Originally Posted by
Dispenser Of Truth
The story really isn't very confusing--just about everything you're asking is in the text, and a lot of it is explicitly stated.
Directly relatively little, though especially with the presence of Ultra Comics it's unquestionable that they've been influencing the proceedings. Thematically, this issue deals with the failure of the super-hero concept, much like the other issues, and it seems very likely Captain Atom (and possibly the Question) will reappear later.
He was collapsed into a black hole and "exited reality". He mentioned earlier/later that he couldn't be killed, and as a man who can see through time he would know. Most likely, he's been merely exiled from Earth 4, to appear later in Multiversity.
He's admittedly more of a plot-driver than anything else (it's not a character-centric piece, aside from President Harley and to a lesser extent Captain Atom), but he's essentially the 'pure' hero this world otherwise lacks, or he at least tries to be. He genuinely wants to make a better world, but his blind faith and violent means to achieve his ends render him ultimately ineffectual.
That was the same guy as who killed the scientists, and she was killed because with Algorithm 8, she could pick up where the President left off or prevent his assassination altogether.
It imparted to the reader information about both the plot and the larger world, showed how his personality had changed over time, and showcased the callous brutality that was the damning flaw of this world's super-people.
By that point, Blue Beetle and Nightshade both pretty clearly thought he had gone nuts and needed to be brought down.
In the original Charlton Comics he was "Sarge Steel", but that's basically irrelevant--the point is that you later see him joining in the Peacemaker's interrogation, making clear he's operating on the orders of the corrupt Vice President. They were killed to prevent knowledge of Captain Atom's demise on the orders of the Vice-President, who didn't trust him and may have known about the conspiracy to kill the President, sabotaging it so he would come to power.
It provides a hint about the VP's involvement in Atom's "death", the mother's dementia and recurring speech is an additional loop, and her references to "the Shadow Dimension" (the Land of Nightshades for the traditional Nightshade, a realm the Multiverse Map clarifies as being in the realm of Nightmare) may become significant later.
Well, it's just going a bit farther forward at first before starting to go back. But it is indeed not totally backwards--Atom shows up again too--the story instead curves in on itself, like a Mobius strip.
He said exactly why he was doing it: after his transformation, he no longer felt the same feelings for the dog he had, and took it apart in the confused hope that seeing its "component parts" would allow him to find his old feelings again (possibly a critique of deconstruction, in that regard). The point is to show how unwell he is, but that like the other 'heroes' he's not meaning to do harm.
It's the scene that informs the rest of the book: it's why Harley went to such lengths to try and save the world and why the heroes were so broken: because he accidentally killed the original and morally greatest super-hero, and his own father at that. It's what shatters him enough to go on the spirit quest that leads to him 'finding' Algorithm 8, the nature of which is shaped at least in part by the domino mask. Additionally, it's been noted that the eye of Intellectron seems to be visible on Harley's fathers drawing board, suggesting that this is where the Gentry interfered with this universe.
Yeah, that's the President, and as well as looking like Jesus, since he's trying to become an "American Christ" of sorts through his death and resurrection as a messiah, he's meant to resemble Alan Moore, since this is a Watchmen reflection. In a lot of ways, Harley is Moore, or at least Morrison's conception of Moore: a brilliant man trying to fix everything by changing the superhero to accommodate it, but despite his brilliance and good intentions, causes more problems than he solves. That's the moment he gets Algorithm 8 and...look, asking why they spend so much time on this guy is like asking why Watchmen keeps flashing back to the Comedian, or why that one movie spends so much time on that dead Kane fella.