It is not that the story doesn't make sense, it is that it is a rehash of several other stories (that have already been told) on a dumbed down and cliched manner. The issue is more so that as a cohesive narrative (which is what stories are supposed to be) it makes little sense why certain parts of the game are there at all, let alone in that order. It feels more like 3arc just had a bunch of ideas for levels and tied them together with a shit line like: "this shit is so meta, it's the -blam!-ing matrix, none of this is actually real, the player will be so surprised that they have been brainwashed/indoctrinated" The twist at the end where the player starts saying the frozen forest dialogue to indicate that his brainbox had finally been indoctrinated...good -blam!-ing job, Mass Effect 3 beat you to that. The flash backs to past battles...shit, they rip off their own crap...black ops 1 did that The whole premise of a serious accident crippling the protagonist and having cybernetic augmentations...Deus Ex And perhaps the bigger issue: HOW THE -blam!- DOES THIS STORY HAVE ANYTHING TO DO WITH THE FIRST TWO GAMES?