Shortly before the Straw Hat Pirates arrived at Jail Island, the Amber Pirates orchestrated an attack on the Amber Harbor to find the treasure on Jail Island. John was injured in the raid, and captain One-Man decided to leave him for dead out of anger.
One Piece: World Seeker
The Amber Pirates stayed in Amber Harbor, and Luffy, Chopper, and Jeanne came to them to help John. One-Man criticized John for getting injured and, after he called John useless, Luffy challenged him. The Amber Pirates fought Luffy but were defeated and forced to retreat. John went back with Luffy and the others to the Thousand Sunny for his treatment.
Later, John tried to defend the Thousand Sunny against Isaac's robots, but Buggy arrived and destroyed them before he could.