We haven't seen the original timeline. We've seen the 'right one' from Peter's POV because it's one in which he existed, but it's not in its original form, what I mean is, the timeline we've seen the past seasons had been rewritten at least twice before. Remember Walter tells Peter when Peter asks him not to send the machine in 'The Day We Died' that he can't do that because it'd be undoing something that he's already done, which means that in a previous state of the same timeline he sent the machine through the wormhole and that automatically rewrote that timeline and led them there, to that situation in which Peter stepped into the machine and destroyed the Redverse.
That previous state of the timeline is what I call the original timeline, the timeline in which Walter effectively sent the machine and rewrote it for the first time.
The one we've seen in previous seasons is a timeline rewritten at least twice, cause there's the machine buried and when Peter steps in it his consciousness is taken forward.
In the original one, the machine is created -allegedly by Walter- in the future, we don't know exactly what year, presumably 2026. When he sends it the timeline rewrites itself. But it's not like going back in time, they actually don't go through everything all over again. Imagine something happens in the past that alters your present reality. Suppose one person gets killed in a car accident cause the driver is having a heart attack while driving. Now suppose too, that in the future you send back in time through a wormhole that opens up somewhere the blueprints of a device that helps prevent and cure any heart disease long before any symptom shows. You won't go back in time like when Alistair Peck sort of 'rewound' the timeline but that thing you sent back in time will change the past and subsequently the present reality. Imagine that now that there's this new diagnose device the doctors would detect and cure any problem the driver might have had while driving, resulting in the driver being healthy and whoever got killed being now safe and sound. You won't see all that happen, but you'll see a new reality in which both the driver and this random person are alive

Anyway, back on topic: he sent the machine, the reality changes, there's a machine that can both create and destroy, but it's not enough, cause they don't have enough information and Peter ends up destroying the Redverse, in this 'second' timeline/once rewritten timeline. We take a peek to this timeline in 'The Day We Died.' We see that sending the machine was not enough, so Peter and Walter find a way to send Peter's consciousness forward when he steps in the machine, say they fix something when they're about to send the machine so that when it's rewritten again the reality changes again. That's the timeline we've seen. One that's been rewritten at least twice. Also it's a timeline in which Peter's existence depends exclusively on the fact that the observer saved him and Walter from drowning in the frozen lake.
But in the original timeline, in one that hasn't been previously modified, ever before (at least not by regular humans; again there's always the observers, of course), in the one Walter creates the machine (to then send it for the first time) Peter had to exist. He couldn't have possibly built it without him because the machine is based on him, on his DNA. His existence then was a fact. What happened after the timeline was rewritten that turned him into a time paradox? we don't know..
Unless....Walter used his DNA to create the machine in the original one (?) and what the machine reacts to is in fact the Y chromosome which is what fathers pass to their sons hence why Walternate could use baby Henry to turn it on on his side(?)
But then of course if he used his DNA to build it that means he could have stepped into it and not use his son right?
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