The Deus Ex script was the first I ever wrote for Playthroughline, so I was really looking forward to tackling Mankind Divided, the next entry in the franchise. I won't use this space to dig into the game's misappropriation of social issues for its science fiction allegory, since the script already does that. I do want to look at how a more general failing of its storyline is connected to the first Deus Ex.
Deus Ex took the prevalent conspiracy theories of its time (the Illuminati, Majestic 12, Area 51, FEMA, Echelon, grey aliens, black helicopters, etc.) and created a world in which they were all true. It took these deliciously pulpy beliefs and successfully unified them into a straight-faced story. This success hamstrung Human Revolution (and by extension, Mankind Divided) in two ways.
First, neither game could repeat this trick because the leftover conspiracy theories and the ones that have popped up since are uniformly lame (The Earth is flat? Jet fuel can't melt steel beams?). Second, since both games were set up as prequels, they had no choice but to lead into the setting of Deus Ex and scale back their own plot developments.
As a result, Human Revolution and Mankind Divided focus on fairly generic conspiracies enacted by the Illuminati and all focused on transhumanism (in the form of mechanical augmentations). I suspect the inevitable sequel to Mankind Divided will allow itself to delve deeper into the backstory of Deus Ex, namely the schism between the Illuminati and MJ12, and Bob Page's ascendancy (as I once figured towards the end of this post).
That's why Mankind Divided's main story is fairly underwhelming: it shows all the signs of a middle entry in a trilogy, which has to maintain a reasonable status quo and reserve more dramatic plot developments for the conclusion. The game really shows its storytelling strength in the sidequests, which show a more human side to its central premise than the overarching schemes of the Illuminati.
The game is significantly helped in this by its detailed level design, which allows stories to be told and clues to be dropped in more subtle ways than the abstracted graphics of Deus Ex ever could. The mechanic in Morgan Everett's Paris compound is a good example. He's been replaced by an MJ12 spy and the player can figure this out (and save Jock's life) by finding the corpse of the real mechanic tucked away in a corner.
Mankind Divided doesn't have to telegraph its clues in such an obvious manner. The various Prague apartments the player can break into organically tell stories of its inhabitants, allowing them to draw their own conclusions instead of having it all spelled out. This isn't a knock against Deus Ex. The limitations of its engine forced the developers to make use of what they had for its environmental storytelling, which couldn't go much further than, say, written messages in datacubes positioned next to corpses.