Unnamed Grandfather (Deceased)
Flannery is identical in appearance to her game counterpart.
Ruby and Sapphire Chapter
Flannery appears alongside Winona, as they greet Norman training his son, Ruby. Winona states that the Pokémon Association sent them to bring Norman back to his Gym, as Flannery reveals that she hasn't been too responsive either. Norman leaves Ruby unconscious on the ground, complying with Flannery and Winona. Later, Flannery trains arduously at the Lavaridge Gym with her Magcargo, as Winona commends her abilities. She informs Flannery that a young trainer has recently come to the Association's attention, who has been able to defeat Brawly, Roxanne and Wattson. Flannery resolves herself to fight against Sapphire, as both Amber and Shelly of Team Aqua appear before her.
The two admins ask whether she knows Sapphire, to which Flannery evades an attack from their Pokémon. Later, when Sapphire arrives at Lavaridge Town, Flannery emerges gagged and bound from a cable car alongside Matt. He thanks Flannery for her helpful advice, as a tear wells in her eye. Sapphire jumps onto the cable car, and realises that Flannery has been severely injured. When Sapphire begins to attack Matt, she is thrown back next to Flannery by the sheer force of his Azumarill's Hydro Pump. As the cable car begins to flood with water, Flannery and Sapphire begin to drown, prompting Matt to protect himself in an air bubble generated by his Azumarill.
Whilst Flannery and Sapphire are unable to move, Matt sends out his Sharpedo to attack them. As Sharpedo moves in to attack, Sapphire pushes Flannery out of the way. Matt is surprised that Flannery is still able to move around, let alone breathe. He sends his Sharpedo around for a second attack, as Sapphire uses her Rono to protect Flannery. However, much to both Flannery and Sapphire's surprise, his Sharpedo's teeth grow back, as Matt proclaims his victory. He reports back to the other Aqua Admins, as the water level begins to decrease, prompting Flannery to gasp for breath. Sapphire reveals that she used his Sharpedo's broken fangs to break a hole in the glass, defeating Matt swiftly with Lairon's Take Down.
As the cable car begins to fall to the ground, Sapphire leaps out, carrying the weakened Flannery. She apologises to Sapphire for revealing her name, but commends her skills as a Pokémon Trainer. As Flannery attempts to pursue the other Team Aqua members, Sapphire inquires as to where she is going. Flannery reveals that their plan must have something to do with Mt. Chimney, and that it is her duty as a Gym Leader to stop them. Sapphire resolves herself to assist Flannery, as the two fly across the terrain on her Tropius. They notice a huge machine situated next to the volcano, as Flannery tells Sapphire to destroy it. However, Shelly attacks them with his Pelipper, as Flannery tells Sapphire to get past him and attack.
Flannery tells Sapphire to use her Tropius' Magical Leaf attack, as the machine becomes primed. They are outmatched by the power of the meteor charging up the machine, as Magma Admin Tabitha intervenes. The two of them pool their powers together, successfully managing to restart the dormant volcano. However, despite their best efforts, Flannery realises that they were only able to temporarily do so, as Tabitha commends her abilities shortly before leaving. When Flannery rejoins Sapphire, she expresses her thanks towards the Trainer. While they are at the hot springs, Flannery requests a battle against Sapphire, which she accepts. However, the battle ends in a draw, as Flannery tells Sapphire that she is going to inform the other Gym Leaders of this new evil that has emerged. She gives Sapphire the Heat Badge as a reward, as the two go their separate ways.
Later, Flannery appears at Fortree City, heading the Gym Leader Conference. When she informs the Gym Leaders of her findings, Flannery sides with Team Magma alongside Wattson and Winona. Roxanne asks Flannery whether Professor Cosmo was sighted alongside the Team Aqua Admins, to which she confirms this. After Norman leaves the meeting, Flannery reveals that their current forces are not sufficient to defeat the rising threat, and that they should call upon the assistance of strong Pokémon Trainers. When Winona arrives at the Tree Tower alongside Sapphire, Flannery and the other Gym Leaders wholeheartedly support the decision to call upon her assistance.
Later, Flannery is present when Team Magma uses Groudon to cause a heat wave rippling through Fortree City. As the crisis unfolds, Flannery teams up with Wattson to prevent Kyogre from advancing further to Sootopolis City. However, when Winona comes under attack from Aqua Admin Shelly, Flannery is forced to assist her mentor. When they team up to fight against Shelly and Matt, they find themselves hopelessly outmatched. When Wattson falls defeated at the hands of Amber, Flannery charges down at them, but is pinned in a chokehold by Shelly's Ludicolo. When Flannery attempts to attack Shelly with her Vulpix, it is easily defeated by Ludicolo's Nature Power ability. When Shelly attempts to finish Flannery off, Winona intervenes, protecting her.
As Shelly orders Ludicolo to finish them off, Winona reveals that during Vulpix's last moments, Flannery had it release Grudge, preventing Ludicolo from attacking with Nature Power. Shelly then realises that she will lose if they continue, and deserts her comrades, as Flannery attempts to follow in her wake. However, Winona prevents her from doing so, explaining to Flannery that there need not be any more sacrifices today. After the conflict has ended, Flannery and the other Gym Leaders welcome Ruby and Sapphire onto the Ba.Goon airship, congratulating them on their achievements. When Flannery returns back to Lavaridge Town, she sees Tabitha walking around the town, much to her surprise.