Native factions will attack any nearby ships that travel through their protected zone territory if the fleet's owner is no longer under the zone's protection. If you have previously left the safe zone to move to another system in the main galaxy, the natives will become hostile to your fleets. On the upside, after leaving you will be able to destroy native fleets and buildings. Destroying native outposts will remove their territory, freeing it up to be claimed by player alliances.