The Baudelaires' investigation into the grotto uncovers a deadly VFD weapon, one which could prove fatal to Sunny. Fiona has a crisis of confidence in her abilities to lead after their capture, and Hookie must make a difficult decision after discovering the Queequeg.
- Adaptational Heroism: Fiona's FaceHeel Turn is clearly shown to be a ruse to help the Baudelaires escape, rather than a true betrayal.
- Damned by Faint Praise: When asked to list Count Olaf's good traits, the best Fernald can give after some thought is "he has a wonderful laugh".
- Find the Cure!: The first half of the episode involves Violet and Klaus having to find a cure for Sunny, who has been infected by the Medusoid Mycelium.
- Grey and Gray Morality: Discussed by Hookie/Fernald, who tells the Baudelaires (who firmly believe in Black and White Morality) that nobody is truly good or evil.Fiona: People aren't wicked or noble. They're like chef's salads.
- Kill It with Fire: The reason Fernald burned down Anwhistle Aquatics was to try and destroy the Medusoid Mycelium.
- Pet the Dog: Mr. Poe wants the Baudelaires to come with him because he believes their innocence and wants to help them prove it.
- The Reveal: We learn Hookie's real name, how he lost his hands, and how he ended up with Count Olaf after being kicked out of the VFD.
- Slave Galley: We learn that Esmé's submarine is powered by the kidnapped snow scouts in this manner.
- Thicker Than Water: Fiona won't escape with the Baudelaires because she doesn't want to abandon Fernald, her only remaining family.
- Where It All Began: The Baudelaires surface on Briny Beach, where the tragic series of events began, and are greeted by Mr. Poe. Lampshaded. However, this time, they refuse to continue it by going with Mr. Poe.Violet: It's like we're starting the cycle all over again.