The Key was a device created by the original designers of the Intersect which was intended to materially alter the Intersect's original function. Since changing the Intersect this way could be dangerous, the key was designed to split into three parts, and a piece was kept by each of the lead designers, Stephen Bartowski, Ted Roark, and Hartley Winterbottom.
Roark's piece, however, handed over to a Fulcrum agent by Roark himself, Hartley's piece, was acquired by The Ring through unknown means; and General Beckman was the recipient of Stephen's piece, who had given it to "someone in the government", it is unclear whether Beckman was the original bearer.
The Key only appears in Chuck Versus the Goodbye when Nicholas Quinn, rogue spy and a disgruntled former CIA agent, is trying to reassembe the key, so he can have the last known clean copy of the Intersect.