The story itself is very basic, a terrorist bombs a train station and you are on a mission to find and stop this terrorist. Simple enough premise and with some inspired writing, this could have been the basis for something larger, a starting point where you begin to pull the threads of the tapestry to revel something more behind the scenes. Sadly, this doesn't happen. You just solve the case, find the terrorist and the game ends. You do travel to different places, deal with different factions and meet different people along the way, but there is no twist, no deeper meaning, no meaningful reveal at the end.
Just like with HR, the game before this one, the creators don't seem to know what they want to do with this franchise. Yet, the game works as a Deus Ex game, and it stands on its own. Very much on its own, in fact, nobody even in shouting distance. Some have (rightly) pointed out that HR was more a Ghost in the Machine game than Deus Ex, this one is more Deus Ex than Ghost in the Machine, but so alone, so far from its origins and ostensible inspiration with regards to the story, that I would question if the executive producers are in fact right for the job. Many plot threads are left hanging, dropped or forgotten when the game ends - only the main thread is concluded.
I vaguely recall the "twist" or whatever being that Manderlay and MJ12 were basically behind the terrorist attack, trying to set up themselves for more power? Maybe I am making that up. I guess it's not much of a twist anyway since HR had the same thing going on. The franchise was obviously being set up for the Dentons being clones of Jensen for his augment accepting genes, and probably a Jensen sacrifice ending of some sort to set up Deus Ex, but yeah I doubt we get there now.