MADISON, Wis. — Raw intimidation.

That’s how one conservative target describes the nearly three-year John Doe investigation into organizations like hers.

The worst part of the politically charged probe, she said, isn’t even that her group has been accused of crimes she insists it did not commit. It is the sense of powerlessness in knowing that she and so many other conservatives, bound by a strict court-administered secrecy order, have no way of defending their reputations.