Perry has always been protective of his naive owners, especially after the mess in the Second Dimension. But when Phineas disappears, secrets won't be able to hide and more than one person's going to have to confront certain demons. In the Dark can be read here.
- A Day in the Limelight: This story is one for Ferb; in fact, that's part of the reason the author gives for Phineas' disappearance from a story-telling perspective: to give Ferb a chance to shine.
- Bigger Bad: Whoever Carl-2 is working for is responsible for every villainous act up to Chapter 16.
- Break the Cutie: Done to poor Phineas-2 off-camera. Possibly also Phineas-1 as well though we've yet to see that.
- Hope Spot: In the Second Dimension, Ferb and Perry finally find Phineas...only it's not their Phineas but rather the one from the Second Dimension who's being blackmailed into working for Carl-2 and the organization he represents. Then they get dragged off to a new prison.
- I Have Your Brother: How Carl-2 and his mysterious boss have kept Phineas-2 working for them.
- My God, What Have I Done?: Candace's response to finding out about the panic caused by her disappearing with most of the neighborhood kids.
- Red Herring: The magazine clipped note seems to point to Doofenshmirtz but he's uninvolved. Another example that's a zigzagged involves Khaka Peu Peu; at first, he seems involved, then he seems cleared and then finally he's part of the posse behind everything.
- Sibling Protective Instinct: Demonstrated by Ferb, Candace and Albert (much to Irving's surprise).
- Would Hurt a Child: Considering Carl-2 and his boss are forcing Phineas-2 to work for them by threatening Ferb-2, yeah; they qualify.