Ruby fished Feefee in Route 118, while helping a Swimmer in order to apologize for messing up his fishing traps. Thinking she was hideous, Ruby threw her back into the river, but she kept coming after his fishing pole despite the fact the Ruby kept throwing Feefee back into the water. When the swimmer realized that Ruby was fishing and discarding Feebas away he explained that, while not knowing the reason, Feebas was very valuable. After learning that, Ruby tried to fish her once more, but was unable to do so. Feefee reappeared when Ruby and the Swimmer were being attacked by Zangoose and Seviper, to return Ruby's PokéNav and ended up protecting them from the two enraged Pokémon.
Seeing that Feefee had protected them and took a liking to Ruby, the Swimmer forced Ruby to keep her. Ruby initially intended to release Feefee as soon as he had the opportunity to but later decided that using such an ugly Pokémon to win the Beauty segment of Pokémon Contests would be a good test to his Coordinator skills. Feefee eventually won both the Verdanturf and Fallarbor Contests. Ruby decided not to use Feefee when he challenged Wallace for an unofficial Contest, however.
Ruby used her again in the Slateport Contest, but by Wallace's request, the judges all voted against her. Ruby, frustrated by Sapphire's words during their last meeting, unleashed his rage in Feefee, saying she didn't deserve to be in his team and kicking her out of it, although he realized soon after that he was wrong to do so and tried to get Feefee back, but to no avail.
Feefee later went all the way to Sootopolis City in order to reunite with Ruby. She was then hurt and humiliated by Archie and Maxie who said such ugly creatures didn't deserve to exist, but Ruby realized Feefee's inner beauty was greater than any external beauty and, after receiving the Beauty Contest Hyper Rank Ribbon from Wallace, gave it to Feefee and finally gave her own introductory speech. Feefee then evolved into Milotic, the Pokémon Ruby has been searching for since he met Mr. Briney and helped in the battle against the two leaders. She later won the Master Rank of Beauty Contests.
She was also used by Ruby in his battle against Emerald in the Battle Dome, but she was defeated by his Sceptile.