A Place Called Armageddon: The Seaquest crew learns that World War III has broken out and the surface is a nuclear wasteland, finding a few survivors and then diving deep to avoid radiation. It turns out to be a hoax planned by UEO brass to see how the crew of the flagship will react, and the survivors are plants. When the crew learns of this, they Troll the plants by pretending to fall so hard for the hoax that they've set the self-destruct rather than attempting to survive on waning supplies in a nuclear apocalypse, and further troll the UEO by cutting communications for a few hours to let them think they'd really gone through with it.
Friends in High Places: Seaquest participates in a wargame during which they are fired on by a live torpedo. The perpetrator's motives are exposing decades-old Cuban war crimes.
About-Face Treatment: Captain Hudson is captured by Macronesia and brainwashed into believing he's The Mole, a longtime spy working for Macronesia to infiltrate the UEO. In a variation, he's made to believe that Oliver Hudson is a real UEO officer that he looks like via plastic surgery, instead of being a supposed long-term infiltrator.
Depths of Deceit: A Gambit Pileup involving President Bourne of Macronesia trying to take over Deon International and their new space-based anti-submarine weapon, while Captain Hudson's father conspired with President Bourne's Dragon to overthrow him and gain control of Macronesia.
The Vault: Several supporting characters are recruited for a dangerous mission while on shore-leave.
Additionally, Jonathan Brandis wrote and was set to direct an episode entitled The Horizon Crew, but the script has never found its way into the internet.