As Flash begins training for his rematch with Thorax, a far greater threat emerges from the shadows and threatens to capture the Pokémon at the Fillydelphia Gardens.
- Badass in Distress: Flash ends up having to rescue Thorax and Pharynx when they get kidnapped by Chrysalis and her men.
- Beauty Equals Goodness: Kingsect and Queensect are both evolved forms of Grubirth, with Kingsect being the male counterpart and Queensect the female counterpart. When Flash sees Queensect, he jokes that "Kingsect won in the looks department", much to the anger of Chrysalis.
- Evil Matriarch: Chrysalis is the mother of Thorax and Pharynx, returning to take over the Fillydelphia Gym and impose her draconian rule over it.
- Sadist Teacher: When Chrysalis used to run the Fillydelphia Gym, she demanded any trainer she beat to give up their Pokémon to her, contrary to a Gym Leader's goal of testing them.
- Screw This, I'm Outta Here: When Flash beats her Queensect, Chrysalis summons multiple Alakazams to teleport her away, while swearing that Flash hasn't seen the last of her.
- Took a Level in Badass: Viper learns Flamethrower when battling Queensect.
- Vagueness Is Coming: When Thorax contacts the other Gym Leaders, it's revealed that Chrysalis' group are members of Team Shadow and everyone is warned of their impending threat, even if little else is revealed about them.
- The Worf Effect: Chrysalis beating Thorax and Pharynx in a Pokémon battle establishes her as a far more powerful trainer than either of them, heightening the stakes of her later confrontation with Flash.
