After a motorcycle accident in 1964 he suffered loss of function of one of his arms and that resulted into losing his chance to return into space. But I presume his not so perfect Mercury flight also might have played a role in the decision to take him off the list for another flight.
He turned into an aquanaut for the Navy in the late sixties, working in underwater laboratories.
|Malcolm Scott Carpenter © NASA|
This leaves his good friend John Glenn the only one still alive of the Original Seven.