During the events of Super Mario RPG: Legend of the Seven Stars, one of the seven Star Pieces crashed into the ocean, and was later recovered by Jonathan Jones and his pirates. When Mario arrives to claim the Star Piece for the Elder of Seaside Town, Johnny states he will only hand over the relic if Mario and his allies can defeat him in battle. The pirate leader starts the fight with four Bandana Blues for protection. After his bodyguards are defeated, Johnny challenges Mario to a one-on-one duel. Alternatively, if Mario leaves at least one Bandana Blue alive, Mario will not have to enter the duel. Additionally, after his HP have dropped below half, Jonathan uses Get Tough! causing Jonathan's skin to turn red and he uses more powerful attacks for the rest of the battle. Mario is eventually able to defeat Jonathan, who then respectfully gives Mario the Star Piece.
When Mario returns to Seaside Town, it is revealed that the Town Elder was in fact Smithy's lieutenant Yaridovich in disguise. Mario is forced to hand over the Star Piece, and Yaridovich runs to the coast to be picked up by the Axem Rangers. However, the Rangers were running late, so Yaridovich decides to swim away (even knowing he would rust). Before he can reach the water, Jonathan Jones and his pirate crew block his exit, forcing him into a confrontation with Mario. Yaridovich is soon defeated by Mario, and after a word of farewell, Jonathan returns to the Sunken Ship.
Jonathan Jones was last seen during Super Mario RPG's ending sequence, standing on the cliff where the Yaridovich battle took place and gazing out onto the sunset. He and his Bandana Reds also operated a float based on the Sunken Ship (moved by King Calamari's tentacles) during the ending parade, and this float was notable for being the first to be affected by nightfall and the glitter released by a Star. ✘