Three years after the first film, Moana continues exploring islands in search of others connected to the ocean. One day, she receives a vision from her ancestor, Tautai Vasa, who reveals that the evil storm god Nalo sank the mystical island of Motufetu, severing the connection between islands. If Moana doesn't restore it, her island will be deserted. Moana assembles a crew from Motunui—craftswoman Loto, Maui fanboy Moni, and grumpy farmer Keke—along with her pet pig and rooster, Pua and Heihei, to find the island.

Meanwhile, Maui is also seeking Motufetu, due to a past conflict with Nalo. He is captured by Nalo's enforcer, Matangi, who is reluctant to harm Moana. Moana’s crew encounters the Kakamora, coconut-like pirates who reveal that Nalo's actions caused them to lose connection with their home island. Kotu, one of the Kakamora, helps them paralyze a giant clam that leads them to Matangi's lair. There, Moana learns that Matangi dislikes serving Nalo and helps Moana escape, reuniting her with Maui and the crew.

Maui warns that Nalo’s realm is dangerous, and fighting him would be suicide. The group is ambushed and stranded on an isolated island. Moana, discouraged, is inspired by Maui to keep going. They plan to raise Motufetu with Moana’s touch, the key to restoring the island and stopping Nalo. As they reach Nalo’s realm, he attacks, stripping Maui of his godhood. Moana, risking her life, touches the island undersea but is killed by Nalo’s storm. Maui, with help from Moana’s ancestors, revives her, and Moana restores Motufetu, reconnecting the ocean with the mortals.

Moana returns home to a hero’s welcome. In a mid-credits scene, Nalo plots revenge with Tamatoa, seeking to get back at Moana.