When Red later met up with Blaine again in And Mewtwo Too?!, he joined him in a battle against the Legendary Genetic Pokémon Mewtwo. Although Mewtwo seemed practically impossible to stop, Red finally managed to use Aero to glide through Mewtwo's Psywave tornado in order to get close enough to send Pika in with Blaine's Master Ball, successfully catching Mewtwo.
In Double Dealing with Deoxys, Aero battled alongside Pika as his last two Pokémon in his battle against Blue. Red had Aero use Take Down on Scizor, which dealt no recoil damage due to his Rock Head Ability. Aero followed up with Dragon Claw on Scizor, so Blue switched him out for Rhydon. Seeing an opening, Red has Pika attack Machamp with an electric attack. To Red's surprise, the attack is suddenly redirected. Blue smirks and reveals that Rhydon has the Lightning Rod Ability, which causes all Electric-type moves to be redirected towards him. Since Pika's Electric attacks had no effect, Pika jumps into the air and delivers an Iron Tail onto Machamp's head. The battle then ends in a tie.
Later Red sent Aero out in his battle against Organism No. 2. However, the DNA Pokémon proved to be too strong for the Fossil Pokémon, as he was first badly slugged by Organism No. 2's powerful punch and then had his wings pierced by Attack Forme Organism No. 2's tentacles. He was soon nearly killed along with Red's other Pokémon while defending his Trainer from Organism No. 2's Psycho Boost. Due to his injuries, Aero had to remain in his Poké Ball afterwards, and as a result, Red had to temporarily trade Blue's Charizard into his team to use as transportation, as Aero could not fly in his current condition.
Aero appears to love the outside as the first thing he did when he got resurrected was to look outside through the window in Blaine's laboratory. He is shown to be reckless as he often rushes into situations without giving it much thought or concern. He is also very generous as he rushed to help Blaine and Gyara even though he had just met Red.