He used to be a proud sailor who loved the sea, but loved his wife Scarlette even more. While he was out at sea, Scarlette became very ill and died shortly after he returned from his voyage. The grief and nightmares caused by her loss made him lose the desire to ever sail again.
Paper Mario: The Thousand-Year Door
In Paper Mario: The Thousand-Year Door, he is needed for navigation to Keelhaul Key, yet he refuses to come. When Mario gets the letter from his late wife Scarlette and gives it to Bobbery, he reads it and learns that she loved him very much, so after a quick change of mind, he comes with Flavio and the rest of the passengers to Keelhaul Key. When he is "dying", he wants a last Chuckola Cola as his wish. When Mario gives him the beverage, he "dies"; actually, he just fell asleep, so Mario woke him up, then Bobbery decided to join Mario's team, going onward to the fifth Crystal Star in Pirate's Grotto, held by Cortez.
He helps Mario in Fahr Outpost by by improving relations between him and the resident Bob-ombs and explaining their situation to the mayor. He also revealed that he's visited the outpost once before, although the details of this visit are left unknown.
After the events of the game, Bobbery decides to join Cortez's crew and returns to sailing the seas for the rest of his days.
Super Paper Mario
In Super Paper Mario, he appears as a Catch Card that is awarded for winning the Duel of 100 in Sammer's Kingdom. He also makes a cameo appearance in the intro cutscene where he, along with all of Mario's partners from the previous two Paper Mario games, are in a photo at the Mario Bros.' House. A plush toy of him can also be seen in Francis' Fortress. He and all of Mario's partners from the previous two games were originally going to appear in the game but were removed for unknown reasons.