Two Years Later

The coated Thousand Sunny submerging.

Two years later, Franky returns to the ship and Bartholomew Kuma, having fulfilled his mission of defending the vessel, left the archipelago. With the planned Straw Hat reunion at Sabaody coming up, Rayleigh coated the ship. Slowly but surely, the crew of the Thousand Sunny came back to Sabaody. Also upon returning to the ship, Franky modified it with what he acquired from Vegapunk's lab. The ship also had a buoyancy sack placed underneath it, so it would not sink once coated. A bubble, caused by Franky redirecting the air in the bag formed around the ship's deck, allowing the Straw Hats to breathe while the ship is submerged. The ship then went under the water and the crew head for Fishman Island.[31]

As the ship was traveling underwater, it came under attack by the Caribou Pirates. Caribou quickly jumps onto the ship. Before the other Caribou Pirates can follow, their seacow, Mohmoo, fled in terror after seeing Nami, Sanji, and Luffy, leaving Caribou on the Thousand Sunny. After the Strawhats tied Caribou up and travel to the Underwater Waterfall, the Thousand Sunny ran into the kraken. The ship went down the waterfall after the Monster Trio defeated the kraken and got separated. After reaching 7000 meters below sea level, the ship was in the Underworld of the Sea. Sunny went through the dark region of the underwater world until it came across the deep-sea volcanic region. There, the Sunny ran into a giant angler fish, an umibozu, the Flying Dutchman, and Vander Decken IX. Before the umibozu knocked down the Sunny, the newly-tamed kraken knocked out the giant. When the undersea volcano started to erupt, the Kraken (now named Surume) carried the ship away from the eruption and jumped into a trench. After reaching 10,000 meters below sea level, the ship finally arrived at Fishman Island. The Straw Hats then encounter a Hammond, a member of the New Fishman Pirates and a gang of sea monsters. Hammond gives the crew two options: join the New Fishman Pirates or have their ship sunk. Luffy rejected Hammond and the fishman prepared to attack. Franky activated Coup de Burst and the Sunny flew through the bubble surrounding Fishman Island. Immediately afterwards, the ship lost its coating and the crew was separated while the ship fell into a current which swept it out to the Sea Forest where it remained while being recoated by Tom's younger brother, Den.

As the king's execution drew near, the Straw Hats make their move. Thousand Sunny flew into Gyoncorde Plaza and Franky shot the Gaon Cannon at the New Fishman Pirates. The ship landed in the plaza, and the Straw Hats and Jinbe stand in front of it, ready for battle. Ussop, Chopper, Nami, and Pappug get into Dock Soldier Four as Franky prepared to reveal one the Sunny's newest weapons.