Epilogue is the level which completes the story of Braid and explains the metaphors in game and the meanings of the characters.
In the end, the game ends where it began.
The boy called for the girl to follow him, and he took her hand. He would protect her; they would make their way through this oppressive castle, fighting off the creatures made of smoke and doubt, escaping to a life of freedom.
The boy wanted to protect the girl. He held her hand, or put his arm around her shoulders in a walking embrace, to help her feel supported and close to him amid the impersonal throngs of Manhattan. They turned and made their way toward the Canal St. subway station, and he picked a path through the jostling crowd.
His arm weighed upon her shoulders, felt constrictive around her neck. “You're burdening me with your ridiculous need,” she said. Or, she said: “You're going the wrong way and you're pulling me with you.” In another time, another place, she said: “Stop yanking on my arm; you're hurting me!”
He worked his ruler and his compass. He inferred. He deduced. He scrutinized the fall of an apple, the twisting of metal orbs hanging from a thread. He was searching for the Princess, and he would not stop until he found her, for he was hungry. He cut rats into pieces to examine their brains, implanted tungsten posts into the skulls of water-starved monkeys.
Ghostly, she stood in front of him and looked into his eyes. “I am here,” she said. “I am here. I want to touch you.” She pleaded: “Look at me!” But he would not see her; he only knew how to look at the outsides of things.
He scrutinized the fall of an apple, the twisting of metal orbs hanging from a thread. Through these clues he would find the Princess, see her face. After an especially fervent night of tinkering, he kneeled behind a bunker in the desert; he held a piece of welder's glass up to his eyes and waited.
On that moment hung eternity. Time stood still. Space contracted to a pinpoint. It was as though the earth had opened and the skies split. One felt as though he had been privileged to witness the Birth of the World…¹
Someone near him said: “It worked.”
Someone else said: “Now we are all sons of bitches.”
She stood tall and majestic. She radiated fury. She shouted: “Who has disturbed me?” But then, anger expelled, she felt the sadness beneath; she let her breath fall softly, like a sigh, like ashes floating gently on the wind.
She couldn't understand why he chose to flirt so closely with the death of the world.
The candy store. Everything he wanted was on the opposite side of that pane of glass. The store was decorated in bright colors, and the scents wafting out drove him crazy. He tried to rush for the door, or just get closer to the glass, but he couldn't. She held him back with great strength. Why would she hold him back? How might he break free of her grasp? He considered violence.
They had been here before on their daily walks. She didn't mind his screams and his shrieks, or the way he yanked painfully on her braid to make her stop. He was too little to know better.
She picked him up and hugged him: “No, baby,” she said. He was shaking. She followed his gaze toward the treats sitting on pillows behind the glass: the chocolate bar and the magnetic monopole, the It-From-Bit and the Ethical Calculus; and so many other things, deeper inside. “Maybe when you're older, baby,” she whispered, setting him back on his feet and leading him home, “Maybe when you're older.”
Every day thereafter, as before, she always walked him on a route that passed in front of the candy store.
He cannot say he has understood all of this. Possibly he's more confused now than ever. But all these moments he's contemplated — something has occurred. The moments feel substantial in his mind, like stones. Kneeling, reaching down toward the closest one, running his hand across it, he finds it smooth, and slightly cold.
He tests the stone's weight; he finds he can lift it, and the others too. He can fit them together to create a foundation, an embankment, a castle.
To build a castle of appropriate size, he will need a great many stones. But what he's got, now, feels like an acceptable start.
Tim is the horrible, evil monster that snatched away The Princess, as described in World 2. The game story hints that he is also alcoholic and cruel. Furthermore, he is a scientist who doesn't hesitate using inhumane methods to reach his aims, like implanting tungsten filaments into water-starved monkeys. To reach this, he mastered time manipulation, only to live in his own reality so he can undo his mistakes. Furthermore, he can be seen as one of the researchers who invented the atom bomb.
From the candy store part, it can be interpreted that Tim's childhood wasn't bright either since he also had pains and obsessions for reaching his aims, even considering violence to get the candies in the candy store. The efforts to make him give up, such as bringing him to the same store everyday, didn't work either.
The Princess represents aims, mostly unreachable, of hard work and effort. According to the story in the game, different interpretations are possible. The most known and popular one along them is that she represents the atom bomb since the hints in Epilogue. Another hint for this interpretation is also her explosion when Tim reaches her, among all the other living things on the level, excluding Tim. Furthermore, the storyline also tells that she radiated fury and Tim chose to flirt so closely with death. The sentence "Now we are all sons of bitches," is also a direct quote from Kenneth Bainbridge after the first successful atom bomb test in New Mexico. Note also the reference to Manhattan; the atomic bomb's development is also known as "The Manhattan Project".
From the storyline, the ending where The Princess explodes could be seen as true ending when she represents the atom bomb since Tim reached The Princess in the end. The other ending where she escaped from Tim successfully and got rescued by a knight would be the fact Tim was trying to prevent all the time. Tim would achieve this by creating a world that flows backwards, represented as World 1.