Okay, so, Transistor.
That game had some Bioshock-level confusion. Lots of questions were left unanswered. However, I have a theory.
Basically, the entire city already was assimilated by the Process. Not just after the game- and not just the city itself. Everything, already.
The Transistor, at its core, is a massive memory chip. It is made to resemble one, and acts the same. It absorbs the data(/mind) of any it makes contact with- either by being 'plugged in', or by touching the remnants.
The remnants appear to be data left over from when a person is killed- which is odd, considering normally when someone dies, their mind doesn't just float over their body, still conscious. So, in at least some function, everybody has a technological aspect to themselves. Either by way of implants, or- and here's what I think- by way of being machines of a sort.
The Process are technological in origin, and can assimilate both the city and people into themselves. They also begin to take human form throughout the game- becoming more and more manlike. If they are able to ease the changes the city makes- as they were originally used for- then why can they also absorb people? Moreover, people aren't the same as the city itself. Unless-
The Transistor is the 'brush', able to shape the city into whatever form is required. But if the Process doesn't just take over the city, but also people themselves, then the Transistor should also be able to shape people.
The Transistor can CREATE HUMAN BEINGS. Or at least, a shape close enough to match. So... it follows that, perhaps, this has happened before.
The Process isn't sentient enough to be able to have 'data', yet, so it cannot have a ()Function when destroyed- at least, not yet. Sybil did, however, even in that warped form, drop one.
I think that the Process has invaded before, wiped the city clean, absorbed all survivors and all construction- and the lone survivor of the city used the Transistor to return it to its original state. I think it's happened before.
Thus, Red's actions in the last moments of the game are that much more significant. Instead of restoring the city, instead of bringing back what had been lost, she broke the cycle. She allowed the city to rest.
This doesn't account for a number of things, of course, so I admit it has flaws. Namely, it doesn't account for the origin of the Transistor or the Process, nor does it account for Red losing her voice. It also doesn't include any place for the Spine, nor for the connection between the Spine and the Transistor. Those could be a separate theory, however, though I find it somewhat unlikely.
However, thematically, it does match what Supergiant did with Bastion. In the final moments of Bastion, the Kid carried Zulf through the streets of the Tazal Terminals, even while being shot and attacked by the Ura. They slowly stop firing, eventually even beating down one of their own who continues to do so. The idea of peace in destruction- of the world being gone, and being allowed to stay gone- that their cataclysm offered them a new chance for the future. The idea of not repeating the past is present in both- in one of the two endings for Bastion, to move on and travel to the mainland- and in Transistor, in Red's falling-on-her-sword, refusing to recreate the city that has already been destroyed.
Thus, I think the two do have a similar theme. That the past should not be repeated. If the city were to just be destroyed again- if civilization would just fall from the sky again, over and over- then it is pointless to do so. The failures of the past should be accepted, learned from, and moved on from.