To be in the dark means not knowing what's going on. Imagine trying to find something in a pitch-black room and you'll understand why it's used that way.
This phrase can be used with a couple of different meanings. Just saying that someone is in the dark means they're unaware of what's happening: "I'm totally in the dark about celebrity gossip these days." If you say something happens in the dark, that means it happens in secret: "She made her political alliances in the dark, aware that voters would not approve."