Deciding whether to side with the Hunter or the Emissary—or with neither—is one of the biggest choices you'll make in Starfield. While the Emissary is seemingly the more peaceful, lawful good option, you might want to consider siding with the Hunter's more chaotic ways. Or you can simply strike out on your own and do whatever you want.
There are pretty significant story spoilers in this guide, so tab away now if you want to go in blind.
Should you side with the Hunter or Emissary?
As you might expect, siding with one Starborn over the other leads to one becoming your enemy at the close of the main questline. The Emissary wants to keep the Unity safe from those it deems unworthy of using it, whereas the Hunter thinks it should be a free-for-all: if someone is powerful enough to claim it, then might makes right. You can also choose to side with neither of them, which means they'll both become your enemy.
When facing either the Hunter, Emissary, or both, you will get an option to persuade them to step aside. While this means avoiding a particularly challenging fight, you won't get a weapon as a reward, so weigh that choice up when it comes. You'll make that decision during the Revelation quest, but you'll be presented with each Starborn's argument during the quest In Their Footsteps, so be sure to exhaust each dialogue option.
Side with the Hunter
If you side with the Hunter, you'll fight the Emissary in the final mission and he'll be there as an NPC follower to help you. Before that, though, you'll need to either kill Keeper Aquilus or convince him to go into hiding. The Hunter is reborn in another universe through the Unity, leaving behind a legacy that wills the many to rise up against power.
There is a Speech option you can use to persuade the Emissary not to fight you, but if you do kill them, you'll get a particle beam rifle called Eternity's Gate, which does increased damage to humans, fires two projectiles on every fourth shot, and has volatile rounds that, if they hit, will do increased damage.
Side with the Emissary
Pick this option and the Emissary will be an NPC ally here, and once the quest ends the Emissary will remain in this universe to seek out individuals worthy of being Starborn.
You'll have to kill or persuade the Hunter, and choosing the former will net you a laser rifle called Unmitigated Violence, which irradiates and frenzies enemies while doing double damage to those with full health. Neat.
Side with neither
You can either talk them both down or fight them both alone, but it is a difficult fight. This ending means humanity can search for Artifacts and use the Unity as they see fit without any interference from the Starborn.
If you choose to fight them, there's a lot of jumping around timelines and fighting duplicates of both the Hunter and Emissary, so it can be quite a tough battle. On the plus side, when you win you'll get both of their weapons as your reward.
Once you've either talked down your foe or wiped them out, it's on to Starfield's ending, which conveniently introduces its New Game+.