The series follows the adventures of a team of scientists on the research vessel called the Calico, which is headed by Captain Carl Majors. The rest of the crew include Dr. Quinn Darien, a female scientist; Broch, her assistant and Carl's first mate; and her teenage nephew Pete. Also along for the ride is Godzooky, the nephew of Godzilla and Pete's best friend who has a light-hearted role in the show. Godzooky can fly using the small wings under his arms, though his uncle Godzilla is unable to fly. Whenever he tries to breath fire, he just coughs up smoke and he never seems to have the ability to shoot laser beams from his eyes. Godzooky is voiced by Don Messick.

The group often call upon Godzilla by using a special communicator when in peril, such as attacks by other giant monsters. If the communicator is not present, or lost, Godzooky uses a special "howl" to summon him. Godzilla's size in the animated series shifts radically, sometimes within a single episode or even one scene. For instance, Godzilla's claw can wrap around a large ship, and only minutes later the team of scientists fit rather neatly on Godzilla's palm. In addition, Godzilla's trademark atomic breath is altered so he breathes simple fire. He can also shoot laser beams from his eyes much like Superman's heat vision.

Season 1 (1978-1979)

1. The Fire Bird (September 9, 1978)
2. The Earth Eater (September 16, 1978)
3. Attack of the Stone Creature (September 23, 1978)
4. The Megavolt Monster (September 30, 1978)
5. The Seaweed Monster (October 7, 1978)
6. The Energy Beast (October 14, 1978)
7. The Colossus of Atlantis (October 21, 1978)
8. The Horror of Forgotten Island (October 28, 1978)
9. Island of Lost Ships (November 4, 1978)
10. The Magnetic Terror (November 11, 1978)
11. The Breeder Beast (November 18, 1978)
12. The Sub-Zero Terror (November 25, 1978)
13. The Time Dragons (December 2, 1978)

Season 2 (1979-1980)

1. Calico Clones (September 15, 1979)
2. Micro Godzilla (September 22, 1979)
3. Ghost Ship (September 29, 1979)
4. The Beast of Storm Island (October 6, 1979)
5. The City in the Clouds (October 13, 1979)
6. The Cyborg Whale (October 20, 1979)
7. Valley of the Giants (October 27, 1979)
8. Moonlode (November 3, 1979)
9. The Golden Guardians (November 10, 1979)
10. The Macro-Beasts (November 17, 1979)
11. Pacific Peril (November 24, 1979)
12. Island of Doom (December 1, 1979)
13. The Deadly Asteroid (December 8, 1979)

• Ted Cassidy - Godzilla
• Jeff David - Captain Carl Majors
• Al Eisenman - Pete
• Hilly Hicks - Brock
• Brenda Thompson - Quinn
• Don Messick - Godzooky/Godzuki