Indigo is a Black Ops program originating in Dimension Two and aimed at exerting influence over Dimension One.
D2 children are chosen and taught to hate Dimension One and to blame them for The Flu that killed off 7% of the human population in Dimension Two.
The children are trained for years as soldiers, with the goal of being inserted into the lives of their D1 counterparts or "Shadows" in order to carry out missions to damage D1.
Because these sleeper agents must be physically identical to their Shadows, the children are required to mimic every aspect of their shadow's life during training. This means if their shadow gets dental braces, they must also get the same appliance. In one extreme case, D2 Clare had to undergo a painful procedure to break both her legs without anesthesia in order to exactly copy the damage her shadow suffered in an accident.