Following the directions illustrated in the Shepherd's Journal, a Viking ship sets forth through a thunderstorm to locate what is believed to be a portal that will lead them to Atlantis. One of the crewman is concerned about the page that shows a giant creature supposedly guarding the entrance, but the captain will hear none of it and threatens to kill any one that tries to halt the expedition any further. Suddenly, a gigantic creature leaps over them before it attacks the ship. Tentacles violently drag crewmen to their watery grave while also tearing the ship apart. The captain shows no fear, but is knocked down from a falling mast. Satisfied at eliminating all aboard the ship, the Leviathan descends into the water before shooting an energy blast that completely destroys the ship. The Shepherd's Journal is hurled several feet away into the ocean, unscathed.
The sequence was part of the film from the beginning. It was designed to illustrate the importance of the Shepherd's Journal, giving it a sense of history so that when it comes into the possession of Milo Thatch the audience will believe it is as valuable as it is claimed to be. Additionally, the filmmakers wanted to start the film off with a bang to make the point that this was not going to be the typical Disney animated feature.
Around March 2000, fairly late into production, the filmmakers held a screening of the film to review their progress. Once the screening had ended, Story Supervisor John Sanford sheepishly stated that the story was not working. He explained that audiences would not be emotionally invested in the Atlanteans, particularly when it would be roughly halfway through the film before they would ever meet them. John boldly suggested that the viking sequence be cut in favor of a whole new opening.
The filmmakers were clearly concerned, given that the prologue had already been completed and had been featured in the first set of trailers. But they believed that John was right and ultimately went with his suggestion that the opening should instead be about the line of dialogue Kidagakash Nedakh says about having witnessed the fall of Atlantis as a child. Later screenings with the new sequence would prove him correct as audiences reacted much better to the Atlanteans.
The viking prologue would ultimately be featured in one of the video games and as bonus material in both the single and double disc editions of the DVD release. On the audio commentary for the film, the directors note that the shield Milo holds up in his presentation rehearsal is the only set piece from the prologue to remain in the final film. It would have been used to illustrate Milo's belief that the Shepherd's Journal would be in Iceland.