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While all of the talk of the Manhattan Project and the atomic bomb does sound plausible, I had a bit of a different take on the story.
In my opinion the story is based heavily in Greek mythology, the story of Andromeda to be specific. Andromeda was the princess of Ethiopia. Her mother, Cassiopeia, was extremely vain and arrogant, claiming to be the most beautiful woman in all the land, even more beautiful than the nymph-daughters of the sea god Nereus, the Nereids. Poseidon, a friend to Nereus, saw fit to punish Cassiopeia for her arrogance by sending a sea monster, Cetus, to ravage the Ethiopian coastline. Cepheus, king of Ethiopia and Andromeda's father, consulted with one of Zeus' oracles in desperate need of a way to save his land from Cetus. Ammon, the oracle, told him that the only way to appease the sea monster was by offering his virgin daughter, Andromeda, as a sacrifice. Andromeda was chained to a rock on the coast to be sacrificed to Cetus, but was rescued by her husband, Perseus. Upon saving Andromeda Perseus killed Cetus, after which the two lived happily, having 8 children and ruling over Ethiopia.
For the purpose of Braid's story, "The Princess" is Andromeda, and Tim believes that he is Perseus, on a quest to save her. Upon the standard completion of the game, without the stars, the true Perseus (the knight at the end) appears to rescue the princess from Tim. Now, with his princess gone, Tim is left to search for meaning, to try and discover who he really is, and so he begins searching tirelessly for his true purpose, which leads to the stars. After obtaining all of the stars, time sees a glimmer of hope outside his house. The princess has become visible in the night sky. Tim goes out to look up at his princess, only to find her with her back to him, chained, awaiting sacrifice. Tim finds that he is below the back of the princess, in the same spot as the constellation of Cetus is located in relation to the constellation Andromeda. After all this time, Tim realizes that he is a monster.
There is also a possibility that Tim is not only a representation of Cetus, but of Phineus as well. According to Greek mythology Andromeda was not meant to marry Perseus. She was betrothed to Phineus first, but did not marry him because she was in love with Perseus. At the wedding of Andromeda and Perseus, Phineus appeared and challenged Perseus, but Perseus was victorious, using the head of the Gorgon to turn Phineus to stone.
This is all purely speculation on my part. I came up with it while bored out of my skull waiting for the cloud on 2-2 to move so that I could get the star there. There are more things to back up the atomic bomb story, but I don't see why the creators couldn't have had both things in mind, right?
I like hearing other interpretations, too, and I think that's part of what makes Braid so interesting and terrific. The fact that people are still thinking about it and trying to put things together about it other than what is the generally accepted theory is a testament to the game's beauty.
Also according to Jonathon Blow: "suggests that the princess represents the atomic bomb, though Blow has stated that there is more than just this interpretation of the story."
From wikipedia cited from here: http://www.podtoid.com/podtoid-66-braidtoid/
So hey, yours could be another interpretation, certainly.