After the ship returned to the Blue Sea and the events the crew experienced in Long Ring Long Land, the Going Merry and its crew had reached the fabled city of water, Water 7. This Venice-like city was renowned for its shipwrights and shipyards. So great were these, that not even pirates dared to attack them at risk of not having their ships repaired or worse. This city was a great opportunity for the Straw Hats in many ways. Ever since the damage caused by the marines during the Straw Hat's escape from Alabasta, the Going Merry had continued to sustain heavy damage caused by a number of events. Even though the crew, most notably Usopp, was able to patch up the Going Merry, the repairs done to the ship were below standard. Here, the Straw Hats could finally fully repair the ship properly. Even better, they also hoped to gain a new member for the crew from the abundance of shipwrights within the city. This they hoped would help maintain the ship fully. With these high hopes, they docked the Going Merry on a shore near the city.
Kaku evaluates the Going Merry's condition.
After renting some Yagara Bulls and exchanging the gold they acquired from Skypiea for a total of Bsymbol.gif300,000,000, Luffy, Nami, and Usopp proceeded to Dock One where they met Kaku,[11] and then later President Iceburg of the Galley-La Company and two other foremen working there. Seeing as they were customers then, Kaku decided to check out their ship. Unfortunately upon returning, the shipwright brought bad news. The Going Merry was now irreparable.
This, as Kaku as explained, was because the keel (which is like a ship's backbone) was broken. This was the most critical part of the Going Merry and it being broken meant the ship could never be fixed again. This meant the ship would practically sink on the way to the next island. Luffy, not wanting to accept this, insisted that the shipwrights repair the ship regardless of the cost. It was then, however, that Luffy and Nami realized that Usopp was missing, along with two-thirds of their money intended to repair the ship. This was done by the Franky Family, a gang of bounty hunters that earlier had attempted to raid the Going Merry with Zoro on it.[12]
After discovering that Usopp had been taken and beaten up by the Franky Family for the money, Luffy, along with Zoro, Sanji, and Chopper, decided to raid the gang's hideout to reclaim the money, as well avenge their fallen comrade. However, when they trashed the place, they discovered that the money that could have been used to repair the ship, had been taken far away from Water 7. With this turn of events and the facts given by the Galley-La company, Luffy made the hard decision to instead buy a new ship. This decision, however, didn't go over well with Usopp. Having repaired the ship so many times, Usopp had come to treasure the ship to a point where he considered it as part of the crew. This he couldn't accept as it seemed to him like the crew was abandoning one of their own. This disagreement with Luffy's decision eventually led to Usopp leaving the crew and a battle between him and Luffy for ownership of the Going Merry. This battle in the night was an intense one for both combatants. This was because Usopp had known Luffy more than the latter's previous opponents, and was able to come up with some strategies to battle Luffy for the ship. However, despite all the effort Usopp put into it, Luffy beats him. Even though he was the victor, Luffy let Usopp keep the ship as an act of pity. The next morning, Luffy and the rest of the crew take their belongings off the ship, leaving Usopp alone with the Going Merry.

After the intense battle from the night before, Usopp continued to desperately repair the Going Merry, despite his lack in carpentry skills and equipment. Eventually, Usopp is "kidnapped" by the boss of the Franky Family, Franky, in order to draw out Luffy whom the latter had a brief battle with. Usopp and the ship are then taken to Franky's secret hideout under the bridge. Despite being enemies, the two bond together and Franky allows Usopp to continue repairing the ship. However, after hearing Usopp plans to use the Going Merry to go back home, Franky began to dismantle the ship despite Usopp's protests. The underworld boss told Usopp the same reason Kaku told him as to why the ship couldn't be repaired anymore. Usopp, knowing this all too well, replied that he knew already that the ship could no longer be repaired but didn't have the heart to accept it. It is then that Usopp revealed to Franky about the mysterious spirit that he saw. Realizing what Usopp was talking about, Franky explained to Usopp that the spirit he saw was a Klabautermann, a manifestation of a ship's soul brought about when it has been loved and cared enough. Franky explained to Usopp that the Going Merry is a ship whose final job now is to carry its crew to one last island before it could sink. Should it not be able to do so, the ship would have failed in its duty. It, he explained, would be happier to simply be dismantled at an island than to sink with its crew onboard. This explanation made Usopp realize how much more of a nakama the ship was. However, it also led to a heated debate between him and Franky on whether or not the ship should be dismantled. Before the debate could get anymore heated, Franky's hideout was breached. The intruders who barged in were Lucci, Kaku, Kalifa, and Blueno, four people who were then revealed to be secret undercover agents of Cipher Pol 9.
After a brief struggle wherein the agents took down Franky in order to get the blueprints of the ancient weapon, Pluton, the Going Merry was put in a dire situation. One of the agents, Kaku, explained that even though he was undercover, his evaluation of the ship's damage was not false. As one last act of him being a shipwright, Kaku casts off the Going Merry out into the sea where the fury of the Aqua Laguna was currently besieging Water 7. With a mighty fall from the hideout, the Going Merry plunged into the raging sea. Its fate then would be unknown until much later.