Seaquest and its crew reappear on earth 10 years after disappearing. The crew has no memory of what happened to them, but their skills and boat are still needed to stop a power hungry President of a new alliance.
The Seaquest gets involved in a businessman's scheme to use refugees and an iceberg to further his financial and political gains. Ben Krieg makes a return as one of the refugees and Dagwood becomes an official member of the crew.
Seaquest is called to investigate missing undersea haulers. Leading the investigation is the Captains ex-fiancé which causes some tension on-board. Dagwood meets other Daggers during the investigation and considers staying with them.
Three members of the crew take a ride on the maiden voyage of an under water high speed train. During the trip a saboteur tries to discredit the new technology by causing an overload in the trains speed.
Henderson is captured and put on trial by Macronesia while rescuing children from a disabled vessel. Once found guilty and sentenced to death some members of Seaquest attempt an unsanctioned rescue attempt.
Max Scully returns, this time as a leader of an underwater colony, but his intentions are far from noble. With the help of Elan Morse, Seaquest tries to stop Scully from detonating a large nuclear waste dump.
A reactor accident sends seaQuest back in time to an alternate 1962, where the Cuban Missile Crisis turned to nuclear war. The only chance to put things right again is to travel further back in time and prevent the first shots from being fired.
On the eve of the signing of the new UEO charter, President Alexander Bourne and Larry Deon conspire to gain control of Lieutenant Fredericks' psyche-implant in order to program her to assassinate Secretary General McGath and cripple the UEO beyond repair.
On a diplomatic mission, Henderson discovers that her former love is now a prisoner and forced to work as slave labour. She also finds that Mason Freeman, Larry Deon's hired gun, is also a prisoner. When the two of them instigate a prison break and steal a submarine, they capture a UEO science outpost and hold the science team hostage.
As seaQuest patrols a free trade zone between the UEO and Macronesia, Lieutenant O'Neill's online romance turns out to be a defector from an elusive Asian power known as the Chaodai, a power that attacks both the UEO and Macronesia with its impressive sub-fighter capability. In this final adventure, one member of SeaQuest's crew will not live to see another day.