Prior to the start of the manga, Kiki was given to Ruby as a Skitty as a gift from his father, Norman. One day, when Ruby was playing with Sapphire, a Salamence attacked them and Ruby sent out Kiki, Nana, and Rara to fend it off. The three managed to scare it away, but Ruby got injured in the process, which scared Sapphire. Because of this incident, Ruby decided to never battle in front of people again. Before moving to Hoenn, Kiki was used by Ruby to win multiple contests in Johto.
Kiki first appeared as a Skitty in Creeping Past Cacnea, where she was seen with Ruby on his trip to Hoenn. After running away from home, Ruby was almost caught by his father while he was helping Wally catch a Pokémon, but was saved by Kiki's Safeguard.
Activating Cute Charm as a Skitty
In Stick This in Your Craw, Crawdaunt! II, Kiki was sent out when a wild Crawdaunt attacked Mr. Briney. His Peeko was unable to battle after her beak was shattered due to Crawdaunt's Shell Armor Ability. After Mr. Briney passed out, Kiki was able to defeat the Crawdaunt by spinning around to avoid damage and increase the chance of activating her Cute Charm Ability. After Crawdaunt was infatuated, Kiki slammed into it with a Double-Edge.
In Guile from Mawile, Ruby went into Granite Cave in order to find a Milotic. During the trip, he is attacked by a group of Mawile and in the fight Kiki and Nana both evolve.
In Hanging Around With Slaking I, Kiki fought alongside Nana against Norman and his Slaking and Vigoroth. Nana fired a Hyper Beam while Kiki attacked with Iron Tail. Despite their strength, Kiki and Nana were easily swept away due to the fact that Norman knew all of Ruby's strategies, as he was the one to teach them to him.
Kiki earning the Super Ribbon
In Mind-Boggling with Medicham, Kiki advanced Ruby through the Normal Rank of the Cuteness Contest. In Going to Eleven with Loudred and Exploud I, Kiki is used alongside Ruby's other Pokémon to battle against Courtney and her Ninetales. Although Ruby had a five-to-one advantage, his team was beaten due to Ninetales having control of nine different fireballs.
In I More Than Like You, Luvdisc I, Kiki advanced Ruby through the Super Rank of the Cuteness Contest. After the contest, Kiki is used in Ruby's battle against Wallace alongside the rest of his team, bar Feefee, and loses.
In Always Keep Whiscash on You for Emergencies, Kiki advanced Ruby through the Hyper Rank of the Cuteness Contest.
In The Beginning of the End with Kyogre & Groudon X, Kiki, alongside Ruby and Sapphire's other Pokémon, are used to battle against Archie and Maxie. Kiki was seen charging at Maxie's Camerupt, but was pushed back by Overheat.
In It All Ends Now VIII, Kiki battled alongside the rest of Ruby and Sapphire's Pokémon against Maxie and Archie. Later that day, Kiki is shown to have won the Master Rank of the Cuteness Contest, wearing a Pink Scarf.
In Slowbro Has an Idea, Kiki appeared alongside the rest of Ruby's team when he was checking to make sure they all survived the crash caused by the Draconid people.