My frothing disregard for black people increases..
Im sure there are other interpretations of it but that one seems to be the one that makes the most amount of sense in context. Although if you play through once not knowing this theory and then a second time while knowing this theory it feels like a totally different story. Pretty ingenious.
Read the Plot Analysis faq on that site that has faqs about games.... I think it's called faqsgame or something...
Anyway, it's pretty in-depth. Explains what the game is about and gives plenty of proof. In a nutshell, Tim's a physicist, the Princess is really the A-Bomb, Tim spends his time trying to make the bomb, and then when he finally does, he realizes he's made a mistake. The game itself is a metaphor of his journey. The difference between the game and reality (Tim's reality, he doesn't represent any of the real life scientists who worked on the bomb) is that the game is in a time loop, forever going forward and back and looping around on itself.
As far as the whole atom bomb concept, this is how I saw it. Tim is a nuclear physicist, whether this be that Morrison guy, I don't know. But throughout the entire game, Tim is searching for world peace, otherwise known as the princess. But at the end of the game, Tim realizes that this entire journey has not brought him closer to world peace but farther and farther away. He then realizes that him, his bomb and the Manhattan Project were never the heroes of the world trying to reach this peace but the enemies and the ones putting this idea in jeopardy. And that this goal will, in fact, never be reached. In other words, the princess is always in another castle. But that's just my two cents. I could go all day with this stuff. Amazing game.