Indigo is a Black Ops program originating in Dimension Two and aimed at exerting influence over Dimension One. The implementation and investigation of the plan forms the center of the Season One plot of the New Starz Original Series Counterpart.
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.
The Strategy Department within the D2 Office of Interchange is controlled by a Board of Directors. A dispute among the directors resulted in approval of a plan to exert "quiet influence" over Dimension One via a black ops program known internally as Indigo.
D2 OI Management is apparently unaware of the program. It is funded through private donations from individuals who blame Dimension One for The Flu epidemic. These fanatics hate D1 for what they perceive as an heretofore unanswered attack.
Clare is a graduate of the Indigo program as well as a former teacher at the school in Potsdam. The episode The Sincerest Form of Flattery spends a great deal of time exploring the school and how it works.