We have a LOT of "appropriated" viral code in our own DNA: "Reverse-transcribed RNA molecules compose a significant portion of the human genome. Many of these RNA molecules were retrovirus genomes either infecting germline cells or having done so in a previous generation but retaining transcriptional activity. This mechanism itself accounts for a quarter of the genomic sequence information of mammals for which there is data."[1]

But that they are now part of us and when they are activated it's not some virus waking up but parts of viruses that we have adapted into doing useful things for out cells.

Viruses can cause significant changes in gene networks (for example oncoviruses usually suppress tumor-suppressing proteins [2] which dramatically affects things downstream), but the changes are not as holistic as I think you are describing them.

Yes point mutations (and viruses) can derail neural networks and that can have far-reaching consequences, but I think these things are accidental in both cases and not some virus plan as I felt you were arguing.

[1] https://www.sciencedirect.com/science/article/pii/S136952741... [2] https://en.wikipedia.org/wiki/Oncovirus