Left at Sabaody

After a little reward from Hatchan and some thanks from Duval for a new face, the crew of the Thousand Sunny were told that the only way to get to Fishman Island was to coat the ship with resin from the Yarukiman Mangrove of the Sabaody Archipelago. Learning about this, the Straw Hats steered the ship to the mangrove and disembarked in order to find a coating mechanic friend of Hatchan's, Silvers Rayleigh, to coat the ship. However, through a series of unexpected events, the crew of the Thousand Sunny ended up causing a large ruckus in mangrove. Fortunately in the midst of the mess they caused, the crew found the mechanic.

Having gotten the aid of Rayleigh, the ship was ready to be coated. However due to the mess that the crew caused, the mangrove was no longer safe. Considering the number of Marine troops and a Marine Admiral that were sent to the mangrove to clean up the mess, the crew decided to temporarily leave the Thousand Sunny in Rayleigh's hands. Knowing that staying on the ship at this time would bring only trouble while the mechanic modified it, the crew thought it best to wait it out in the mangrove as the mechanic did his job. Giving the crew his Vivre Card since he'd be taking the Thousand Sunny somewhere else, Rayleigh promised to return the ship after three days of work.[30]

In the midst of the modifications of the ship, the coating mechanic left the ship in the care of the Rosy Life Riders in Grove 41 to save the Straw Hats from Kizaru. Despite Rayleigh's involvement, the Straw Hats were blasted off by Kuma to different locations. With its crew gone, the Thousand Sunny was left in the care of Rayleigh and the Rosy Life Riders until the Straw Hats could return.

After the Whitebeard War, due to Luffy being revealed as Dragon's son, the Thousand Sunny came under attack by various people such as the Coffee Monkeys. Fortunately however, Duval and his men fended them off as best they can. Kuma arrives to the Sabaody with one mission: protecting the Thousand Sunny. After Duval and Hatchan were seriously injured during a battle with the Marines, Kuma took over as the protector.