Spoilers para o fim de Deus Ex:
The "D" in "Alex D" stands for Denton. Like JC, Alex is cloned from Paul and grown in a vat in Area 51. In Deus Ex you find the vat labelled "Alex Denton" towards the end of the game.
E a revolução humana:
Megan is recruited to work on the nano-augmentation project and presumably uses her research on Adam's unique augmentation compatibility to work on the design of Paul and JC.