An experimental submarine escapes from its moorings and manages to launch its nuclear weapons targeted at New Cape Quest, a city with 5 million inhabitants including relatives of the seaQuest crew.

In order to gain control of seaQuest's nuclear weapons, a powerful psychic plants a nightmare in both Piccolo and Dagwood's minds, so that he will be invited on board to interpret their dreams.

Captain Hudson is ordered to blow up an iceberg that has been directed towards Saudi Arabia by a corrupt businessman, only to find a group of refugees placed on the iceberg to prevent its destruction.

Captain Bridger seeks seaQuest's help to go deep into Macronesian waters and retrieve some top secret data crystals that reveal unspeakable atrocities committed against humanity 20 years earlier.

The crimes in which Bridger and Ford may have been involved.

As the world leaders debate the renewal of the UEO charter a number of assassination attempts are made against the delegates.