The group finally arrives at the Crystal Empire and meet up with the professors, Shining Armor, and Sombra. While exploring the wonders of the long lost city, everyone starts discussing recent encounters with Team Shadow and what they might be planning, right as Team Shadow begin their siege on the Crystal Empire.
- All Your Base Are Belong to Us: Team Shadow begin their invasion of the Crystal Empire at the end of the chapter.
- Death by Origin Story: Both of Sombra's parents died in a plane crash when he was just a baby while they were on a business trip. Sombra survived, and was taken in by a group of wild Absol who failed to stop the crash.
- Dramatic Irony: When everyone begins discussing Team Shadow's recent activies and begin putting together what they are up to, they are doing this right in front of Team Shadow's leader, Sombra.
- Early-Bird Cameo: When everyone is looking at the stain glass windows depicting the Legendary Pokémon, the only one shown that has not appeared in the series yet is Centirek, who later plays a major role in Pokémon the Movie: Rival and Darkness.
- Expy: Androrg is one of Andromon. Fitting considering that its pre-evolutions, Higear and Guardroid, were already ones of Hagurumon and Guardromon respectively.
- Internal Reveal: Sombra learns of the various encounters Flash and his friends have had with Legendary Pokémon, including how Flash, Doc, and Twilight were all chosen by the three heralds.
- The Mole: Because Sombra is in good standings with the professors, unlike the rest of Team Shadow, he is able to enter the Crystal Empire without issue, get past the security force, and secretly implant a virus into Androrg that messes with its security list and turns the entire security force against the professors and Flash's group.
- Oh, Crap!: Sombra has a silent version when everyone begins discussing Team Shadow, giving small signs of panic like flinching a bit and putting his hands in his pockets. Nobody picks up on any of these though.
- Raised by Wolves: Sombra reveals that after both his parents died in a plane crash, he was raised by a group of wild Absol until he was twleve and a group of humans found them, with his adoptive family urging him to go with them and be with his own kind again.
- Saying Too Much: When Sombra tries to discreetly throw everyone off Team Shadow's trail, he tries to say that everything they have discussed is just speculation, and that the remaining half of the Crystal Heart may be buried outside of the empire instead of being from the Hidden Temple. But he accidentally calls it a "Heart Fragment" instead, a term that the others have not used yet. Luna notices this, but simply brushes it off, saying "that's another good name for it".
- Surrounded by Idiots: Chysalis call the grunts idiots when they can't find a way through the Guardroid security force.
