That far in the future and they forget the "Cut" and "Paste" commands

[Lazoriss]

Guess that would be why they're brain scans, and not files from the start. Each brain scan stored on a computer is based off a template of a physical brain. The seat would scan the brain, and a computer program would then take that scan and construct an AI that closely resembles the thought process/personality/ect of the original. It explains how an experimental scan from 2015 became the complex character we play as in the game. The scan of Simon's physical brain was used in AI research, basically designing computer programs that could perfectly emulate a "person" using a picture of a brain. The program would then store the emulation as a computer file. In this mode, you can "cut" and "paste" the file.

Omicron is actually kinda weird, because the file for Simon's brain is already in the cortex chip. But the seat never directly hooks up to said chip, instead scanning it. I'm not exactly sure how the pilot seat was able to get an exact copy of the file by scanning the chip. What would make the most sense is that Simon's brain is already on file at Omicron. Catherine just puts you in the seat to activate the new bot and to keep diving suit Simon pacified/asleep in the chair. Perhaps so the experience isn't quite as traumatic for the two Simons involved.

VIDEO GAME LOGIC