You don’t get a lot of opportunities for mid to large-scale battles in Fallout 4. It’s rather unfortunate for a game with a number of warring factions. However, the Battle of Bunker Hill looks to test your allegiance to whichever faction you choose to side with.
If you don’t really care about allegiance, then you can simply kill whoever you want and score some nice loot from either faction. When we say nice loot, we mean gatling lasers, fusions, fusion cells, gauss rifles, and the works, so make sure you go with plenty of inventory space for you and your companion.
However, if you do want to be a snitch, you can head up to the Prydwen and tell Elder Maxson who will order you to kill the synths. Alternatively, you can go to the Railroad and tell Desdemona, who will tell you to free the synths. It’s really dependent on how you choose to roleplay your character and who you choose to side with. Regardless of who you tell, all of the factions will be there at the Battle of Bunker Hill. After finishing the Synth Retention main quest for the Institute, then, speaking to Father will flag the Battle of Bunker Hill.
After talking to the synth outside (who is your ally at first until you decide to make some anti-synth decisions) you can either choose to participate in the firefight, or head down to the basement to either reactivate the synths to go back with the course, kill the courser and free the synths, or just kill everyone.
Your actions really depend on who you wish to side with in the end. For example, letting the synths free won’t really damage your reputation with either faction, but killing the courser and letting the synths free will put you in good with the Railroad.
After you’ve participated in the Battle of Bunker Hill, you can speak to Father who either banishes you from the Institute or praises you and keeps you in good standing with the Institute.
If you’re having difficulties in this battle, consider boosting your armor with the ballistic weave material while also unlocking the mod for it! Plus, we think your gaming experience can be enhanced with mods you never knew you needed!