Salamence rampaging through the Pokémon Association
Prior to the start of the series, Rayquaza was being held prisoner and experimented on by the Pokémon Association in order to create an artificial Orb to control it, as seen in a flashback in The Beginning of the End with Kyogre & Groudon XIV. Zinnia eventually found out and had Salamence infiltrate the association in order to rescue it. Before getting to Rayquaza, however, it ran into Ruby and Sapphire as they were playing together. Upon seeing them, Salamence charges at them and tries to bite them, but Ruby grabs Sapphire and gets them out of the way. Ruby then sends out Nana, Kiki, and Rara, who attack Salamence and deal heavy damage to it. Salamence recovers and strikes Ruby with Dragon Claw, giving him a bloody head. Ruby ignores the pain and gets Kiki to attack with Double-Edge. Salamence, finally having enough, runs off. After the battle, Ruby realized that, because of his aggressiveness, he caused Sapphire to cry, while Sapphire realized that because she was weak, she caused Ruby to get hurt. Because of this, Ruby decided to focus on beauty and quit battles, while Sapphire learned how to become stronger.
Salamence quickly arrived where Rayquaza was and went on a rampage from the pain it had from its injuries. Due to the lack of Trainers there, Salamence destroyed the restraining mechanism holding Rayquaza, allowing it to break free and escape. Salamence passed out shortly after. When Norman arrived, he took a closer look at Salamence and realized that Ruby was the one who injured Salamence. Because of this, Norman took the blame for what happened. As a result, he was punished by being unable to become a Gym Leader for five years and made to track down Rayquaza.
Salamence was also used by Zinnia to defend herself when she infiltrated Team Magma and Team Aqua.
In PS598, Salamence returned alongside its Trainer, Zinnia, inside the Sky Pillar. Deciding that Ruby and Latios were a threat, she sent out Salamence to take care of them, who struck them with a powerful Dragon Claw. It then followed up with a Fire Blast, but Ruby managed to distract Aster and grab hold of Zinnia, forcing it to focus its attack toward Ruby. After getting Ruby off of her, Zinnia precedes to Mega Evolve Salamence, causing it to take little damage from Latios. Ruby and Latios decide to Mega Evolve as well. Salamence then attacks with Hyper Voice, which deals Flying-type damage due to its Ability, Aerilate. Despite the powerful attack, Latios survives and strikes Salamence multiple times before finishing Salamence off with Luster Purge. After the battle, Zinnia revealed to Ruby that Salamence was the one that attacked him nine years ago and thanks him for his help in the matter.
In PS608, Salamence battled in a Double Battle alongside Goodra against Sapphire's Aggron, Rono, and her Gallade, Kirly. Salamence was able to attack Rono with Fire Fang but took all the damage back and more from Metal Burst. The battle was stopped when Zinnia fled for the rocket that Devon Corporation launched. Sapphire followed her with Troppy and attacked with Leaf Tornado. Salamence attacks Sapphire and Troppy and defeats them, allowing Zinnia to destroy the rocket and the dimensional shifter.
Salamence and Zinnia
In PS615, Salamence battled alongside Aster's Noivern to battle against Rara and Kirly in order to take back Rayquaza from Ruby and Sapphire. Salamence attacked the two with Dragon Pulse, but Rara used Misty Terrain to half the damage. Despite this, Noivern hit the two with Boomburst and knocked them out. Zinnia attempted to form a bond with Rayquaza, but it rejected her and stabbed her in the stomach. It then blasted Zinnia and Salamence and sent them falling into the ocean. Salamence was last seen in PS616 with Rono, watching Zinnia talk with Ruby and Sapphire.
Personality and characteristics
Salamence is usually very reserved and observational, but becomes impatient and enraged when it takes too much damage. It has a close relationship with its Trainer and Zinnia highly trusts Salamence, shown when she sent it to free Rayquaza by itself. It is the powerhouse of Zinnia's team and is often used by her as a means of escape.