Professor Kukui/Manga/PA

Professor Kukui debuts in The Delivery of Rotom and the Girl. He is first seen at his laboratory, where he tested the moves of his and. The attacks caused Kukui to be sent flying through the roof and land in front of his house.

There, Kukui encountered and, the latter of which was tasked with delivering a  to Kukui. Kukui explained that he needed Rotom, which aren’t found in Alola, because they are capable of combining with Sun’s Pokédex. When Rotom attempted to go inside the Pokédex, it ran away because the Pokédex was dirty and smelled bad due to Sun constantly mishandling it. Angered by this, Kukui forced Sun to retrieve Rotom while he cleaned the Pokédex. Later that night, Sun returned to Kukui's house with Rotom.

The next day, a sleep-deprived Kukui angrily asked Sun why he wasn’t informed about Sun’s encounter with the previous day. To Sun’s annoyance, Kukui also revealed that he decided to enter Sun in a tournament being held at an Iki Town festival later that day.

In The Decision and the Tournament of Six, Kukui participated in the Iki Town festival tournament while disguised as the Masked Royal. In the first round, Kukui was paired up against Sun. Due to the lack of a monetary reward, Sun refused to take the battle seriously until Hala revealed the prize for winning the tournament, an island challenge amulet. Assuming the amulet was valuable and he could sell it money, Sun became motivated enough to battle seriously, allowing him to win the battle and advance to the next round. Afterward, Kukui watched the remaining battles alongside Hala.

In The Final Match and a Surprising Finale!, Kukui, as himself, transported Sun and Moon to Akala Island on his yacht. While they traveled, Kukui allowed Moon to take his, as he noticed the bond the two developed. Moon also revealed that the Rotom she delivered actually fused with a spare Pokédex she received from Kukui to become the Rotom Pokédex. After arriving at Akala Island, Kukui told Sun and Moon to wait on the docks while he went to the Dimensional Research Lab to talk to his wife, Professor Burnet.

In Going Ashore and Neighboring Akala Island, Kukui sent several Pokémon documents to Burnet, who was still at Kukui’s house. As they talked, Burnet revealed that Nebby is actually the Legendary Pokémon. Burnet suggests that Lillie may have been trying to keep Nebby away from someone, but she refused to clarify who she was trying to escape from. To Kukui’s surprise, Burnet suggested that he make Lillie his assistant, as it may help her begin to open up more.

In PASM14, Kukui arrived at Konikoni City, where he, Sun, Moon, Kiawe, Mallow, and Lana went to Mallow's restaurant, where they talked to Burnet over a video phone. Burnet revealed that earlier that day, she witnessed Nebby clawing at the sky, creating a crack in the sky in the process. With this information, everyone came to the conclusion that the various cracks seen around Alola were caused by Nebby and that Lillie must have been running away from some villains in order to keep Nebby away from them. Worried that Burnet may not be able to keep Lillie safe alone, Kukui suggested Burnet take Lillie with her to meet up with him, Sun, and Moon at Ula'ula Island. To his shock, Lana stated that she and the other Captains will head to Team Skull's hideout in Po Town to have a discussion with them.

In PASM15, Burnet and Lillie used Mantine Surf to travel over the water to Kukui's yacht as it heads off to Ula'ula. Shortly after they arrive, the group is attacked by a wild, which uses its psychic powers to give everyone headaches and pass out. Although Sun successfully rescues Lillie, who was knocked into the water, he and Lillie end up passing out as well and are separated from the others. Later, Burnet, Kukui, and Moon are rescued by the Aether Foundation and taken to Aether Paradise. There, they meet Faba and Wicke, who explain what happened to everyone and offer to give a tour of Aether Paradise.

In PASM19, after leaving Aether Paradise, Kukui, Burnet, and Moon take Kukui's yacht to Ula'ula Island. Kukui, sensing a strange change in the atmosphere, fears that a battle may have started in the hour since the Captains' group arrived at Po Town. With nowhere to dock the yacht, Moon told Kukui to get as close to Ula'ula as he can while she has Rowlet carry her to Po Town by flying through the air. After finding a place to dock, Kukui and Burnet met back up with Sun and Moon in Po Town. Kukui gave Sun one of the Mirage Berries that was left behind on the yacht so that Sun and Moon could feed it to.

In PASM22, Kukui, Molayne, Sophocles, Acerola, and Gladion fought off and  at  to prevent them from reaching Hokulani Observatory, which was being used as a shelter for those caught up in the Ultra Beasts' rampage. Gladion managed to easily defeat Celesteela, but was distracted when Lillie appeared and called out to him, allowing Guzzlord to attack. Gladion's easily defeated Guzzlord and evolved into a  in the process. To Kukui and the others' surprise, Gladion and Lillie revealed themselves to be brother and sister as well as the children of Aether Foundation President, Lusamine. Lillie explained that three months ago, she stole Nebby from Lusamine in order to prevent her from using its power to further her plans. When Lillie presented a Sun Flute she also took from Aether Paradise, Gladion decided that they should head to the altar.