The backstory and continuity of the Deus Ex series are complex to the point of confusion. When you have multiple shadowy organisations, mysterious characters controlling puppet governments, and a cornucopia of conspiracies running alongside all of this, things can get confusing.

With

The mechanical apartheid

All of this is pointing to the notion that Mankind Divided may have much stronger tie-ins to the original Deus Ex. Jensen's destruction of Panchaea left the Illuminati with the ability to create Daedalus, and his DNA is likely facilitating the creation of the Gray Death and later nanoaugmentation itself. There's a reason Megan Reed is shown in Mankind Divided's first trailer: it's only through her actions at the end of Human Revolution that the future of the Deus Ex universe can come to pass. With public opinion on mechanical augmentation split down the middle, the time is ripe for the shadowy cabals to make their next move. How this happens is something we'll have to wait for Mankind Divided to find out. And as the achievement you earn by finishing Human Revolution is called "The D Project", and has a picture of JC Denton's face, it's highly likely we'll see Jensen and the Dentons' lives begin to cross.