Early on, Johns added detail to the backstory of how Dr. Manhattan changed the DCU by deleting the Alan Scott Green Lantern from its history; this is something I sketched out in my review of DC #3 as matching "the subplot of a JLA/JSA crossover in which an evil Johnny Thunder on Earth One used the Thunderbolt to prevent the Justice League from existing." Just as the Thunderbolt in that story prevented, for example, the lightning that gave Barry Allen from striking his lab, Dr. Manhattan in this story prevented Alan Scott from obtaining his lantern (and, moreover, causing his death). We can be sure that most if not all JSAers were similarly interfered with.
With a scene that looked almost literally like a set stage, DC #7 was centered around a group meeting (after a brief, frantic battle) that put Mime, Marionette, the Comedian, New Rorschach, Veidt, Batman, and the Joker together with Dr. Manhattan. And what followed was, for the most part, talk. In the meantime, Dr. Manhattan teleported the Watchmen Universe members of the group to three different times and places, as significant backdrops of relevance that was not stated directly. First, they go to an idyllic nature scene by a waterfall. Then, to an anti-superhero riot at night in Washington, D.C. Finally, they enter a movie theatre in 1954, terrifying the audience seeing the final Nathaniel Dusk film, The Adjournment. And during this time, with a lot of talking and a couple of one-sided fist-fights, something big happens. What is not immediately clear is: What is that something big?
Dr. Manhattan says "No" to Veidt's request. That happens immediately, and seems obviously irrevocable. There is a little more discussion, including the revelation that Veidt was lying about his brain cancer in order to manipulate Reggie into assisting him. (In retrospect, this was foreshadowed by the Veidt jigsaw puzzle that Reggie was working a couple of issues ago. In one frame, Veidt's head had a piece missing. Then Reggie put the correct piece in place and said that it was in front of him the whole time.)
But this is a big scene for some reason besides those. We know this because when Veidt returns to the Owlship, he believes that he no longer needs Dr. Manhattan's help, and that he has a plan to save everybody. These thoughts frighten Saturn Girl, who believed at the beginning of the issue that everything would turn out fine, but at the end believes that Veidt's new plan will ruin everything. This is yet another turn in her demeanor as seen during "The Button" and makes the details of her mental state an important part of the picture.
Why? Whatever Dr. Manhattan said or did changed Veidt's plan is the mystery in front of us the whole time. It was cryptic for us, and we know things that most of the characters don't. We know that the Nathaniel Dusk movies are tied in some way to the JSA-era superheroes, but Veidt presumably does not know that. So what did Dr. Manhattan say that instantly changed Veidt's worldview?
Dr. Manhattan says a few things with a lot of implications, and some pithy but key statements of his concern the two children of Mime and Marionette. Those statements tell us a lot and tell Veidt a lot, too, but not necessarily the same things. First, we find out that Marionette is pregnant again, which means that the child was conceived in the past few hours in the DCU. Second, we find out that their first child will do or has done something that is so significant to Dr. Manhattan that it is for that child's sake that he spared Marionette's life during the bank robbery we saw in DC #2.
If the information that suddenly changes Veidt's worldview is this, then why? Very likely, because Veidt has some reason to suspect that that child would not have a valuable future ahead of him. And we can guess at several reasons why. First, there was a nuclear war happening on the Watchmen Earth when last we saw it, and that is reason enough. Perhaps Veidt even knows from the child's location that he is dead due to the nuclear attack. Also, the photo of the child that New Rorschach gave to Marionette was "a few years old": Perhaps the child died between 1987 and 1992. In any of these scenarios, Dr. Manhattan's statement may give Veidt hope that the entire timeline can be altered. And therefore, it gives Veidt hope that the past can be changed for the better. This is likely the information and motive behind his current plan.
Dr. Manhattan's comments and thoughts also tell us a lot about Dr. Manhattan's plan. First, we find out that he prevented the rise of the JSA through the murder of Alan Scott. In the same passage, introducing the issue, we find out that one of the events in Alan Scott's timeline of which Dr. Manhattan was aware was the JSA's surrender to HUAC, causing the superheroes of the DCU to disappear. Second, we find out that he was greatly dispirited by the death of Colman Carver, which led him to say that his comment at the end of Watchmen was wrong, and that "Nothing ever ends" has been replaced in his worldview by "Everything ends." Why? The connection here likely lies in the inconspicuous details of DC #3's end notes about Colman Carver and a simple panel at the beginning of that issue. According to those references, the screenwriter of Carver's 1947 movie went to prison for refusing to cooperate with HUAC. This was in fact a real man, Ring Lardner, Jr. who really was imprisoned and then blacklisted from Hollywood just as the fictional DC #3 says. Why include this information? This is likely the key as to why Johns has included the Colman Carver subplot in Doomsday Clock. Knowing that HUAC exists in the current DCU timeline, we also know that the same threat that caused the JSA to retire was not dissipated by Dr. Manhattan's alteration to the timeline entailed by the death of Alan Scott. We now know that killing Alan Scott was not a petty or malevolent act on Dr. Manhattan's part, but a calculated one intended to bring about a positive outcome. And this tells us a lot about Dr. Manhattan's and Johns' intentions:
The notion of an entire generation of Golden Age heroes retiring due to pressure from HUAC was introduced in 1979 as I noted in my review of DC #4. This is an idea that Alan Moore copied in Watchmen, with Hooded Justice retiring (like Alan Scott) and Mothman (a major focus of that issue) ending up in a sanatorium (like Lardner). Mothman remembers this when, after Veidt's scheme killing millions is revealed, he says "They're rounding them up" in reference to the events of 1992. Mothman remembers when his generation, also, was rounded up.
And Dr. Manhattan remembers, too. He was discouraged by the lack of hope in both the Watchmen and post-Infinite Crisis DCU timelines entailed by the surrender of the heroes to the political pressures of their respective times. Removing Alan Scott prevented the JSA from existing, and therefore from surrendering to HUAC. But the death of Colman Carver extinguished the hope that Dr. Manhattan found in that. Why? Here, I see two possibilities, not mutually exclusive. One, based on no more information than an offhand comment early in DC #3, that Carver was regarded by Johnny Thunder's fellow inmate Donald as a hero suggests that Carver resisted the political pressures but remained working and in fact subsequently won an Oscar. A second, as I mentioned earlier, is that Carver actually is one of the would-be JSAers, likely Hourman (obsessed with clocks), and his movies had inspired positive heroism, until his death (being beaten to death with his own trophy like Watchmen's original Nite Owl).
And this tells us what is driving Dr. Manhattan. He, too, is driven by hope. He has been altering the timeline of the DCU, trying to achieve a more hopeful outcome. He deleted Alan Scott's Green Lantern career, trying to prevent the surrender of the JSA (which resembled a sad occurrence on his own world), but it didn't work, culminating with the death of Colman Carver. And now, he is seeing how the events finally play out, with Superman, the current symbol of hope, in some future act of war against Dr. Manhattan himself. This is fated to fail, and at that point, Dr. Manhattan ends the current timeline. The post-Flashpoint DCU is an experiment that Dr. Manhattan is running and he (and Johns) deem it a failure, set to end a month from now. The now-explicable scene at the end of DC #1 showing the deaths of the Kents shows another Dr. Manhattan-triggered tragedy that edited the timeline for the sake of an experiment that turned out tragic. When Dr. M (and Johns) give up on the current timeline, some version of the previous timeline, with Alan Scott living and the JSA existing will prevail. And, by implication, we will also get the Kents back. The fistfight between Superman and Dr. Manhattan will not end with the punch making contact, but with the implied sense of malaise leading the entire timeline to come to a dour close.
In the background, another, probably far less consequential mystery concerns the "identity" of Dr. Manhattan in the DCU. We get three clues. One, Dr. Manhattan himself says that he thought he "might find a place among" the DCU. Two, he says that he stood (physically) on the set of The Adjournment in 1954. Third, Bubastis' eyes glow when he is staring in the direction of The Comedian. I don't see a clear resolution behind all these details, but I do see a misdirection. Veidt believes that his cat responds to The Comedian, but New Bubastis already faced The Comedian and had no such response in DC #3. Either the trace of Dr. Manhattan on The Comedian's body happened after that or Bubastis isn't responding to The Comedian at all but to the man who happens to be standing behind him – The Joker. But we see The Joker still standing there after Dr. Manhattan manifests, so The Joker can't be him, as I postulated earlier, but is possibly "on" him in some fashion, or has left his trace there. I don't see how the details shake out yet, but there is some connection between the old movie set (predating most or all of our current DCU adults) and The Comedian and/or The Joker.
Still, whatever the small details, the large details are now apparent. We know Dr. Manhattan's actions and motives and where they lead. We also know that Veidt has a different plan and it isn't the one that Saturn Girl is hoping for, no doubt leading to her horror in the opening scenes of "The Button." Veidt's new plan is supposed to fail, then, and hope lies elsewhere.
And on the note of hope, the theme I mentioned earlier is emphasized once again: Batman comes across very poorly in DC #7. Although he manages to show his competence in battle, it is with mixed results, as he is injured by Marionette and then sucker-zapped by The Joker. Dr. Manhattan takes us to an anti-Batman riot in Washington and, though Batman is the last man standing after the fistfights of DC #7, he comes across as a mere brawler achieving temporary victories while Superman is "the most hopeful." Veidt, Dr. Manhattan, and Johns are all seeking hope. And we hear again and again that Batman is not it; Superman is.