I believe the execution has been more due to the circumstances of recent events rather than a proper plan being executed by stages...
For one, the AI can't act by itself against other humans (apparently?), so she can only wait for orders.
The protocol they have in place requires them to have the cptn relay the orders, if they cannot be contacted for a certain amount of time, the next in command takes charge, which appears to be the current situation.
The AI then asks the next in command to either step in or it will take charge (which contradicts the first step somehow?)
Since the enemy has already breached the 4th wall, the first line of defense, we won't know if there was anything there to prevent a breach besides the walls.
We now have the second in command activating one of the Active Defense Mechanisms, which calls in the local fauna.