many people on youtube have stated that in the bunker that you enter in the alternate ending was where the farmer was situated. it is said that the farmer was controlling the whole goverment program. i think that the farmer realised that what the facility was doing was wrong and decided to try to shutdown the mind control experiment. he may have learnt that the goverment found out what he was doing, he probably knew that he didnt have long to shut down the experiment so he planted the orbs. he programmed the orbs so that when all of them were destroyed, they would give the protaganist the musical code to open the door in the bunker. i also think that the goverment threw the farmer when they caught him into the huddle. when the protaganist enters the game, the farmer, inside the hive mind, controls the boy to disable the orbs. when the protaganist disables the orbs he heads to the bunker in the cornfield. he enters the bunker and enters the musical code into the door. when he enters the room he heads to the cord. on the way he sees the HUB of the experiment and the desk withe the PC and chair at it, proving the farmer was orginally there. he then reaches the plug and pulls on it, thus pulling out of the port. when this is done, the will of the farmer has been complete and the experiment as well as the protaganist, shut down and the boy takes the stance of the drones. i think that the boy was speacially created by the farmer to shutdown the goverment experiment. when the experiment is shutdown, the boy is no longer needed and the huddle loses control on him. therefore, the boy takes the stance of the drones.
p.s for those who didnt know, if you turn left in the bunker, there is a room where the farmer did his reseach. this room is where he also developed photos. on the line if you look closely ( do this in game because on you tube its hard to make out) you can see a photo of the huddle.