21-year-old Cooke who featured in all of Wycombe's Christmas and New Year fixtures has gone back to Villa Park nursing an ankle injury a few days before the end of his one month loan.
Wycombe boss John Gorman, who didn't rule out a new approach for the player, believed it was in the player's best interests to return to the Premiership club for treatment.
"Stephen loved it here and once he recovers we would be looking to take him on," said Gorman.
Lions chairman Theo Paphitis wants Craig back at the end of an impressive loan spell for Wycombe. The 19-year-old will have made 18 consecutive appearances for the Chairboys since October before his return to the New Den on January 22.
However, should Craig continue in the Millwall reserves, Wycombe will try to prise the defender back to the Causeway next season.
"The players, the staff and the fans have all been great. I'm definitely interested in coming back," said Craig.