Winona flew on her Altaria with Flannery and faced Norman, warning him he was absent from the Gym for a long time. Winona and Altaria were present during the Gym Leaders' meeting in Fortree City.
Altaria was used by Winona in her Gym Battle against Sapphire. Sapphire's Combusken, Chic, attempted to attack, but Altaria dodged. Altaria retaliated with Dragon Breath, but Chic evaded the attack. Instead, Chic used Double Team and surrounded Altaria and attacked it, knocking it on the ground. Since Sapphire had trained Chic for a long time, Chic evolved into a Blaziken and used Blaze Kick. Altaria got hit, but just as Sapphire thought she won, Altaria disappeared into the clouds. From there, Altaria used Sky Attack and knocked Chic off a cliff and defeated her. Later on, Winona started her training with Sapphire, who had Chic use Blaze Kick on Altaria, who avoided the attack. The training was cancelled, as Winona received a report and went to investigate with Altaria.
Due to Groudon and Kyogre's presence in Hoenn, Winona flew on her Altaria, along with Sapphire and her Tropius, to investigate to the place where the floods and droughts collided. After Sapphire was saved from the wave, Altaria took her away to a safe place. Winona continued flying on Altaria, as she and Sapphire spoke to the guardians of the Red and Blue Orbs. Before departing away on Altaria, Winona shook hands with Wallace.
Winona went to Wattson and Flannery to assist them in battle. There, she faced Team Aqua admins and had Altaria attack them with Dragon Breath. After Winona's Skarmory affected the Aqua admins with Metal Sound, Altaria burned them with Flamethrower. Winona and Altaria continued their battle and faced Matt. Seeing Wattson drowning, Winona wanted Altaria to rescue him. However, Altaria was focused more on Sharpedo, who distracted it with Taunt. Matt and his Vibrava went to attack Winona and Altaria, who evaded their attacks.
Later on, Winona flew on Altaria to Sootopolis City. There, as a part of the plan to get the Red and Blue Orbs out of Maxie and Archie, Altaria took position. Ruby and Sapphire's Swampert and Blaziken launched their attacks through the meteorite, which were reflected from Wallace's aircar and Winona's Altaria onto Maxie and Archie, which forced the Orbs to be dropped out of their bodies. However, the incoming explosion engulfed Winona and Altaria, who were blown away.
Due to the meteorite threat, Winona flew on Altaria and joined the other Gym Leaders and the Elite Four to stop the collision.
|Dragon Breath +||I Dare Ya, Altaria... Knock Chic off My Shoulder|
|Sky Attack||I Dare Ya, Altaria... Knock Chic off My Shoulder|
|Refresh||I Dare Ya, Altaria... Knock Chic off My Shoulder|
|Dragon Dance||I Dare Ya, Altaria... Knock Chic off My Shoulder|
|Flamethrower +||Bravo, Vibrava|
|+ indicates this Pokémon used this move recently.*|
- indicates this Pokémon normally can't use this move.
- ^ RS031: Hanging Around With Slaking III
- ^ RS042: Short Shift for Shiftry
- ^ RS046: I Dare Ya, Altaria... Knock Chic off My Shoulder
- ^ RS047: I'm Always Grumpig First Thing in the Morning I
- ^ RS055: The Beginning of the End with Kyogre & Groudon III
- ^ RS056: The Beginning of the End with Kyogre & Groudon IV
- ^ RS057: The Beginning of the End with Kyogre & Groudon V
- ^ RS059: The Beginning of the End with Kyogre & Groudon VII
- ^ RS065: Bravo, Vibrava
- ^ RS066: Can I Ninjask You a Question?
- ^ RS067: The Beginning of the End with Kyogre & Groudon IX
- ^ RS070: The Beginning of the End with Kyogre & Groudon XII
- ^ RS072: The Beginning of the End with Kyogre & Groudon XIV
- ^ RS073: A Royal Rumble with Regirock, Regice and Registeel I
- ^ ORAS021