The idea of the ending of season 1 ripped off the idea of the ending of Watchmen, in that
someone tries to "save the world" by destroying New York
I googled for info on the new ending of Watchmen, and since there's a LOT of confusion on it, and since I just discovered spoiler tags, THIS is the truth on the ending:
In the graphic novel, Adrian Veidt/Ozymandias has created a monstrous psychic creature that he makes suddenly appear in New York, which sends out a psychic wave killing half the people in the city, whereupon everyone in the world, on the brink of nuclear war, believes that an alien attack is imminent, thus making everyone band together and end war with the constant threat of an alien attack. But throughout the novel, it's discovered that Veidt has taken hostage many different people to an island for some reason I was never quite clear on, and that's how the Comedian found out about the plan, which is why he was killed at the beginning of the novel.
In the new ending, Veidt has been working with Dr. Manhattan throughout the film, supposedly to create a machine that uses the unique qualities of Dr. Manhattan's physical makeup and "powers" as a form of clean energy that will replace all current forms. But in reality, he's creating a machine to imitate Dr. Manhattan's energy signature that will also create a blast powerful enough to destroy a major city. Then, and this is also in the novel, he frames Dr. Manhattan, making it appear that he causes others to develop cancer, alienating him from the world and causing him to leave Earth, while making everyone in the world distrust him. In the end, he uses his device to destroy major cities around the world in a manner that imitates Dr. Manhattan. Since Dr. Manhattan is gone, everyone assumes that they are under constant threat of annihilation by Dr. Manhattan, and thus everyone bands together, ending war like in the novel's ending.
But the real important part of the novel's ending is that Rorschach had more or less figured everything out and had written it down in his journal, which he later mailed to a newspaper before going off to stop Veidt, later being killed. The last frame of the comic shows a guy at the newspaper offices, his boss desperate for new material, picking up Rorschach's journal, ending with the possibility of Veidt's utopia being undone. This WILL be retained in the movie. So, even though the mechanism of the ending is changed, the message is still the same.
I figured I'd explain it since most websites seem to think that Veidt convinces Dr. Manhattan himself to destroy the cities, which doesn't make any sense and makes it sound like the writer had no idea what the hell he was doing.