And here's the part where I kinda have to ruin the film for everyone, myself included.
In thinking about this film weeks ago, it was obvious the Christian allegories throughout. Flynn acting as a kind of Jesus against the lurid red devil of the MCP. After all, Flynn even performs "miracles" normal programs could not perform. He re-rezzes a Recognizer, even diverts an energy beam for the light sailor. He even prevents Lori from de-rezzing herself.