Cassidy Williams forms an uneasy alliance with Scooby and the gang after her radio station is destroyed by German Kriegstaufen robots. Their lead as to their originations lead them to an underwater city in a trench near Crystal Cove. To get there, Daphne recruits the two boys she used to babysit—Tom and Tubb from the 1967 Moby Dick And Mighty Mightor cartoon show, along with their pet seal Scooby.
The episode provides examples of:
- Ambiguously Gay: Daphne notes that Tom and Tubb's fathers are Dr. Paul Williams and Captain Michael Murphy, but it's not clarified if Tom and Tubb are brothers in this continuity or if she means Tom's father is Paul and Tubb's father is Murphy.
- Continuity Nod: Cassidy had previously used CDs as an offensive weapon in "Revenge of the Man Crab" and "Pawn of Shadows".
- Crossover: Much like "Mystery Solvers Club Finals" the gang meets with Tom and Tubb from Moby Dick and Mighty Mightor. Their parents are revealed to be Dr. Paul Williams and Captain Michael Murphy from Sealab 2020.
- Dead All Along: The gang discovers Abigail Gluck's decayed corpse, even though the programming is still running. However, the word "Nibiru" is whispered from Gluck's lips.
- Downer Ending: Professor Pericles makes off with piece no. 6 of the Planispheric Disc, and it is implied that Cassidy did not survive the detonation of the city instigated by Pericles.
- Get A Hold Of Yourself Man: After they fall into a trap and are at risk of drowning, Fred is ecstatic and tingling because he's focusing on what a good trap this is. Daphne slaps him to get him to focus on finding a solution.
- Heroic Sacrifice: Cassidy Williams dies saving Mystery Incorporated from the blast.
- Last Request: Cassidy tells Daphne to not make the same mistakes she did.
- Little "No": Daphne when all Scooby the Seal finds of Cassidy is a broken helmet.
- Monster of the Week: The Kriegstaffebots, Nazi robots that have been attacking Cassidy Williams for a week.
- Never Say "Die": When Fred says he's sure that Cassidy made it out.
- No Indoor Voice: Tom and Tubb shout all of their dialogue, due to "water in the ears".
- Noodle Incident: While the others go on ahead, Daphne asks Tom and Tubb if they'll be fine on their own. They say yes, citing a time their father left them on a reef for two weeks. They survived by sucking on sea urchins.
- No Swastikas: The "World War II-Era Robots" as everyone calls them, resemble German stormtroopers, speak in broken German, and have red symbols that resemble the "no smoking" sign in place of swastikas on their helmets.
- Not So Above It All: When Cassidy claims her station exploded because of "faulty wiring", Mayor Nettles indignantly asks Sheriff Stone why he isn't going to investigate further. When he points out that accepting the excuse means they can turn the crater into a new public pool for the town, Nettles promptly changes her tune and declares the case closed.
- Official Couple: It looks as if Mayor Nettles and Sheriff Stone are headed that way.
- One-Steve Limit: Averted. Here, Scooby-Doo meets a seal named Scooby.
- Properly Paranoid: The group stumbles onto a nursery of baby robots. Fred insists they keep moving because a baby robot is still one of the enemy. The baby robot that Scooby-Doo is cradling immediately alerts the bigger robots to their presence.
- Shipper on Deck: Cassidy remarks she always thought Fred and Daphne made a good couple. She gives Daphne some advice about relationships and regrets.
- Shout-Out: The title is reference to both the real-life term as well as The Twilight Zone (1959).
- Title Drop: Tom and Tubb explain that "The Midnight Zone" is an area so far down that there is no light.
- Unusually Uninteresting Sight: Averted. The group is creeped out by the corpse whispering a name.
- Wham Shot: Scooby the Seal showing the broken helmet.
- You Meddling Kids: Pericles actually uses the original phrase, but in a sarcastic manner as he does get away with it.
- Scooby: She saved us.
Velma: I guess maybe... we were wrong about Cassidy.
