As the badly damaged Nautilus was sinking in the ocean from an attack by a warship, 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 then decided the only thing to do was to travel to the surface, and fight the squid hand-to-hand. As they prepared for battle and surfaced in the middle of of a raging storm, Nemo instructed his crew that they would be facing the "most tenacious of all sea beasts", to stay clear of the tentacles, and to aim for the spot between the squid's eyes in order to kill it.
Nemo and his crew ventured onto the deck to fight the squid, taking a side hatch as the squid attempted to send tentacles down the main entry hatch to grab the crew. Nemo was soon caught by one of the squid's tentacles after trying to harpoon it himself, but was saved by the first mate and his crew in the battle, only to be caught again during the fight. Meanwhile, Ned Land, having managed to get onto the deck, joined in the fight after being informed by one of the crew of the squid's attack and threw a harpoon at the beast, hitting it right between the eyes and killing it outright. He then dived in as the squid sank beneath the waves and managed to cut Nemo free of the its tentacles before it could posthumously drown him.
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.