So this theory might have been posted by someon so please tell me if there are any other similar theories. To start the theory is about what metaphors Kojima put into this game.

As you might know Kojima likes retelling events of his life in this game. My idea is that this game is talking about his departure from Konami and his way of handling the aftermath. These are in my opinion certain character's and what they represent. Obviously Sam represents Kojima, Bridges and most of supporting cast are Kojima productions and his friends. President Strand/Amalee and the terrorists are Konami and most importantly BT's are his and others traumas and memories.

Finally ill start what i think the major events. So Sam at the start burns the President's body which represents him forgetting his past and moving on. Even though he forgot about his past with Konami and started his company some good and bad things stayed in his life represented by Amalee and Higgs. To skim this theory down ill skip most of the story which is Sam building the UCA and it represents Kojima building his company. The next point ill stop at is a lot farther in the story and it is the boss fight with the EE that and all the events up until the encounter with Amalee is supposed to represent some past traumas catching up with him and Kojima fighting them off. The ending itself is Kojima reminiscing about his past and setting him self free of his past burdens and traumas. The reason I say reminiscing is because I believe Sam and BB are the same person something like President Strand and Amalee.

So this is the theory I hope you enjoyed it.