Pilot Episode

The pilot episode "Eleven Days to Zero" was filmed in colour but shown in black and white. It introduces the audience to the futuristic nuclear submarine S.S.R.N. Seaview and the lead members of her crew, including the designer and builder of the submarine Admiral Harriman Nelson (Richard Basehart), and Commander Lee Crane (David Hedison), who becomes the Seaview's Captain after the murder of her original commanding officer.

The submarine is based at the Nelson Institute of Marine Research (NIMR) in Santa Barbara, California, and is often moored some 500 feet below NIMR in a secret underground submarine pen carved out of solid rock. The Seaview is officially for undersea marine research and visits many exotic locations in the seven seas, but its secret mission is to defend the planet from all world and extraterrestrial threats[1] in the then-future of the 1980s.

Season One

Adm. Nelson and Capt. Phillips are attacked after leaving the Nelson Institute of Marine Research.

The first season of 32 episodes began with Admiral Nelson and the crew of the Seaview fighting against a foreign government in order to prevent a world-threatening earthquake, continuing with a foreign government destroying American submarines with new technologies in The Fear Makers and The Enemies. The season also had several ocean peril stories in which the Seaview crew spent the episode dealing with the normal perils of the sea. Two examples are "Submarine Sunk Here" and "The Ghost of Moby Dick".[2] The season introduced the diving bell and a mini-submarine, as well as the first alien story and the first sea monsters. The season ended with the Seaview crew fighting a foreign government to save a defence weapon.

In the first season, the gritty, atmospheric, and intense series featured story lines devoted to Cold War themes, as well as excursions into near-future speculative fiction. Many episodes involved espionage and sci-fi elements. While aliens and sea monsters, not to mention dinosaurs, did become the subject of episodes, the primary villains were hostile foreign governments. While fantastic, there was a semblance of reality in the scripts.

Season Two

The second season began with a trip inside a whale, a trip inside a volcano, and a few Cold War intrigue and nuclear war-themed episodes, and saw several brushes with world disaster. The season ended with a ghost story, one of the show's few sequels.

Due to ABC's demands for a somewhat "lighter" tone to the series, the second season saw an increase in monster-of-the-week type plots, yet there were still some episodes that harkened back to the tone of the first season. The second season also saw a change from black and white to colour. The beginning of the second season saw the permanent replacement of Chief "Curly" Jones with Chief Sharkey, due to the death of Henry Kulky, who portrayed Chief Jones.

The most important change in the series occurred during this season when a slightly redesigned Seaview was introduced, along with the Flying Sub. The Flying Sub was a yellow, two-man mini-submarine with passenger capacity, that could leave the ocean and function as an airplane. The Flying Sub was referred to by the initials FS-1. The futuristic craft greatly increased Seaview crews' travel options. The Flying Sub was launched from a bay in the lower part of Seaview that was apparently built between Seasons One and Two. The Seaview’s private observation deck from the first season was never seen again. The Seaview’s eight observation windows became four. The Seaview’s enlisted men were also given more colourful uniforms (red or light blue jumpsuits), evidently to take advantage of the changeover from black and white to colour. The officers and petty officers, however, retained their khaki works from the first season. The traditional sailor uniforms worn in the first season were only seen in stock footage from the first season and on characters who were newly filmed to match up with that footage. All these changes occurred between seasons. The Flying Sub was showcased in the show's closing credits for the entire season.

Season Three

The third season of Voyage to the Bottom of the Sea ran simultaneously with two other Allen-produced television series: the second season of Lost in Space and the premiere (and only) season of The Time Tunnel.

The third season began with Dick Tufeld of Lost in Space playing an evil disembodied brain from outer space. The season continued with a werewolf story that is one of the few episodes to inspire a sequel. In one episode, the Seaview’s officers and crew encountered Nazis who believed World War II was still ongoing. The third season only had two espionage stories and one ocean peril story that were reminiscent of the first season. One of those three stories was about a hostile foreign government trying to steal a strange new mineral with the aid of a brainwashed Admiral Nelson. This espionage story was the end of the third season.

Fourth and final season

Nelson and Sharkey fight an alien spy, 1968.

The fourth and final season of Voyage began with Victor Jory playing a five century old alchemist. After a few episodes there were revamped opening credits. Near the end of the fourth season, there were three unrelated stories of extraterrestrial invasion in three weeks. There were two time travel stories in two weeks. The second of the two had the Seaview going back in time to the American Revolution. The episode ended with the Seaview returning to the present and sailing into television history.

In March 1968 it was announced that Voyage would not be back for a fifth season.