The basis for ENDWeapon control, the consciousness synchronization apparatus, or CSA, allows an ENDWeapon pilot to have his consciousness transmitted to a proxy brain inside his ENDWeapon by forming an instantaneous synchronization of the entirety of the pilot’s native and proxy brains via quantum entanglement. For proper functioning, the pilot must undergo a period of suspended animation, during which time his entire brain is mapped and replicated into a proxy brain. This neurological map is then written into the CSA for both brains, giving them a language by which to synchronize each other. Once fully mapped and replicated, the brains are then reactivated in synchronization.
The pilot’s brain state is, of course, dynamic, thus a constant connection between the two brains is necessary, as any lapse in synchronization would render the proxy brain useless. However, as supported by dream science, the human consciousness is not known to be able to be fully aware of multiple realities simultaneously. This means that even though the two brains are paired continuously, the consciousness can only be wholly devoted to one body at a time: either the pilot’s own body or his ENDWeapon. This exchange of consciousness can be mostly controlled through medicine, by inducing either REM sleep or wakefulness. When a synchronized pilot enters REM sleep, his consciousness gravitates toward control of his ENDWeapon, instead of the usual dream state. In order to take full control of his ENDWeapon, however, the pilot must learn to achieve lucid dreaming, otherwise he will not be able to function rationally while in control of his Weapon. While medicine can provide support for the parts of the brain used in realizing one is dreaming, the pilot is ultimately in control of the state of his consciousness. Though the natural limit to REM sleep cycles is approximately 90 minutes, it can be artificially sustained for up to several hours, allowing for the execution of much more substantial missions.
Psst! Here's a non-nerd version.
1 - Yes, I know you can't actually use quantum entanglement to build an ansible. But most people don't.