In one of my storylines, I want the player to attack an enemy. But the enemy should not be destroyed/killed. When the enemy is heavily damaged/wounded, the enemy should become neutral and a conversation should start. How am I able to do that?
It's a work around, but you can spawn in a damaged ship after the battle. It might be a little noticed, especially if the battle moved from it's main spawn point, but right now there's not much else out there.
If there are enough ships in the enemy fleet, you could have the broken ship already there- it may not be noticed until the battle is over.