After playing the game a few times I was still confused. Then people who paid very close attention to the story brought it to the light. We as the Player on the first mission, which was secretly the last mission(not counting the second mission) didn't make it during the procedure. But after death, we see and relive Taylor's memories. The soldiers we see were actually replacing other Black Ops soldiers. For example, Dylan Stone was the enemy. Taylor and Hendricks took him out but Taylor was injured by a knife, resulting in his voluntary Cybernetics surgery. Kane was Rachel the whole time. She left that scarf on the table we see after completing New World. And notice how the days don't change for half of the game until Lotus Towers. The final mission of the game Taylor probably had a virus in his DNI. Perhaps we were helping him wipe the virus. This game took a complete turn around as we saw first hand that the mirror in the Frozen Forest when it shifted from us to Taylor. Taylor literally said what we were thinking: "What the fuck?". We even saw him screaming, probably from trauma. The last part is what I'm thinking though. When you think about it the concept of the story is complex and deep but well hidden.