The Proto Generator is a unique ANMC in that it doesn't attack Aya but it is protected by several Watchers and a control panel (which has 250 HP) must be destroyed before attacking it, otherwise it will regenerate all damage. As the name implies, it is a Generator ANMC, along with the Beta Generator.
The only problem with the fight is the status ailments caused by the Watchers and they should be destroyed quickly. The control panel does not attack but needs to be destroyed to take out the Life Support system. Otherwise this fight is extremely basic as the Proto Generator does not attack Aya.
The Proto Generator reduces all incoming damage by (at least) 90%, has a quick HP regeneration and cannot be taken below 1HP while the Life Support system is active. In order to finish the battle, it must be destroyed, first.
If the Watchers were turned off in the Pod Service Gantry, there will be nothing protecting the generator.