A badly damaged Nautilus was sinking in the ocean. After Captain Nemo's crew managed to stabilize the submarine, Nemo realized that they had gone "deeper than any man has gone before". The squid then moved towards the submarine. They were initially able to repel it with an electric charge, but the damage the submarine had taken made it harder to withstand the squid, and the electrical elements burned out on its next attack. Nemo decided the only thing to do was to travel to the surface, and fight the squid hand-to-hand.
Nemo and his crew went onto the deck to fight the squid. Nemo was soon caught in one of the squid's tentacles after trying to harpoon it himself, but was saved by the first mate, only to be caught again during the fight. Meanwhile, Ned Land managed to get onto the deck and threw a harpoon at the squid, hitting it right between the eyes, killing it outright. He then managed to cut Nemo free of the squid's tentacles.
In a TV special made to promote the film, Walt Disney stated that "It's the squid who is the real villain." He also said that Peter Lorre, who plays Conseil, claimed "the squid got the part that's usually reserved for him".
The original version of the scene took place during sunset. It was ultimately rejected, and was eventually replaced with the version which appeared in the final movie. The 16mm footage of the original scene is still intact, miraculously having survived being burned, and an edited version with added background music is available on the Special Edition DVD.
The original animatronic squid was of similar color to real giant squid, being red. However, this animatronic was difficult and clumsy to operate, and it had several major malfunctions; chunks of the tentacles would fall off during filming and the wires that operated and supported them were too visible during filming because of the lighting. The second model, which was black, was superior in construction, with specially designed tentacles that could move and coil like snakes thanks to hydraulics and air pumps. Due to its black color and problems with the original sunset backdrop, it was decided that the stormy scene that appeared in the final film would be used.
In the original novel, the Nautilus crew was supposed to lose one of their men due to the giant squid's attack before it was killed.