Future!Peter POW, but I'm really just borrowing him as a narrator for my theories about the time loops, with a twist (I hope) at the end.
Unbetaed, English is not my language, all mistakes are mine. Fringe is not, unfortunately.
Puzzles.
Puzzles. Most people have not patience enough or simply see no reason in wasting time putting together the pieces of a picture already drawn, especially if one can buy it in one piece with less trouble. Others crave so much the challenge of identifying and understanding every single piece's nuances that in the end they are not even able to see the whole picture anymore.
Walter has, without a doubt, always been part of the second category. Bodies, machines, life, people, time, the world -hell, worlds- have been mere tools for him to play around with for years, to the point of losing sight of the original canvas. As much as Peter loved his strange second father, he couldn't deny his guilts: Walter - and Bell too - have broken both worlds and shaken them up, scattering and misplacing the pieces all around to the point that no one knew anymore what went where.
How many times have they looped it all already? How many loops ago did they forget where they came from and where they wanted to go to? Have "they" always been the same people "they" were now?
Peter certainly hoped not. Because if he had always been part of the equation it meant that sending back the machine had always ended up with the destruction of both worlds, that he had lost Olivia every time, and that he had never saved nor was ever going to save her.
He had to hope that Walter was right, that by witnessing what was going to happen he could change the single action that led to the destruction of his whole world, and two dimensions as well.
Peter had come to believe that there had been one single loop in which he had lost his life-mate. He would not had allowed it to happen another time.
In time he had formulated a precise theory: in the previous loop (P-1 as Walter had called it, proudly pointing that P stood both for Present and Peter, and that the current loop had to be called P-0 for obvious reasons) Walter had badly messed up with the machine and they had discovered Olivia's powers too late, so they had sent back the picture of the Vacuum connected to both Peter and Olivia in hope that they could fare better with it in the next loop.
He believed that in the same loop Walter himself had decided to take the Machine out of his own hands: why else did he design a way to make his next-loop self ask Bell to remove parts of his brain?
The cortexiphan trials too must have been put in the picture in the P-1 loop: Walter and Bell had designed the ZFT manuscript to ensure that Olivia were "powered-up" and able to deal with things to come at the very best of her capabilities. He could not -would not- deal with the idea that his father had made she suffer through the trials for and undefined numbers of loops already, because it was already difficult to accept the fact that all the other children had been involved by mere commodity.
The Machine, like Nina Sharp pointed once, had clearly been designed by Bell. He and Walter must have started traveling to the Other Side out of curiosity or greed, and after realizing the very texture of the dimensions was broken they probably spent the rest of their lives to find a solution. That vortex through time was their one-way ticket to redemption, Fate's last attempt at mending their mistakes. Too bad that the birthing loop of the Machine will always remain a mystery.
It must have been a hell of a challenge to design a way to pass through time the coordinates of the pieces so that the Machine could be put together only by themselves at the right time, so much that Walter had not been able to figure it out in the current loop. But it was of no consequence, because that seed had already been planted into the loops and it needed not be changed. Peter could only hope it was the same way for all the instructions Bell had seemed to follow, because the old bastard was not there anymore to sent them to his next-loop self.
The Beacon instead had had to be sent back together with the Machine: smart move, to create a sonic drill capable of roaming the planet virtually without touching it and go on undamaged for millions of years. No wonder the Observers and Walter had been so keen of making sure it wasn't stopped: without it the pieces of the Machine would have not stayed were they were supposed to, and no one would have been able to find them.
Walter had gone as far as embedding part of his consciousness into the Beacon just to make sure his future self wouldn't take it apart - like his instincts always told him to - in the next loop: after all he already did it, and it worked.
It was impossible to discern how many loops there had been already, and if the Machine was conceived as a mending tool - albeit misunderstood - or directly as a weapon. Impossible to figure out at which point Bell decided to live on the Other Side in the hope to stop Walter from destroying it, in which loop Walternate had come in contact with the instructions and the Machine, or when Walter had started kidnapping Peter from his homeworld. The only relevant truth was that whatever was done in each one of those loops had never worked.
Peter had never been part of either group. Oh, he felt the challenge, but didn't see the point of putting back together the pieces of the puzzle in their preconfigured, static way. He liked to take things apart and create new ones, make them his own.
He had needed to understand every single piece of this interdimensional time-loop puzzle and never forget the final picture, in order to broke it and reshape it anew so the worlds could exist and his Olivia be alive.
Peter had never been more motivated before. There he was, his flesh and blood self, entering the Machine with love in his heart and hope in his soul, but with no idea of what he had to do in his mind.
He would solve that. The brain porting had worked well, the Machine had carried and shielded his consciousness for millions of years just so he could meet this other version of himself here, now, and become one with him. The reason why Peter was the only one who could operate the Machine had nothing to do with DNA, or predestination, or fate. It had to be him because he was already inside of it: his flesh brain will be able to withstand the contact and the flood of information like no other person in the worlds could. He will last enough to understand what to do, and act on it.
And there she is. In the last moments when Man and Machine touch, when they both can see and feel and understand it all, he can finally have his reward.