The novelization contains four sections:

The first section covers Yuugi solving the Millennium Puzzle.

The second section covers Yuugi's first encounter with Seto Kaiba from the manga.

The third section covers the second encounter with Kaiba in Kaiba Land. It omits many areas that don't deal with the card game.

The fourth section is an original story, occurring only in the novel. Two weeks after Yuugi's battle with Kaiba in Kaiba Land, Yuugi gets a call from Kaiba, who tells him to meet for a Duel at the top floor of the KaibaCorp. Yuugi accepts, and when the duel begins, they use a special variation called the "Bingo Rule," which prevents the used of a specific card in each player's deck. Kaiba seems to be himself, but plays a different trump card, the "Automatic Giant."

Mokuba stumbles in on them, and tells Yuugi that Kaiba has not yet awoken from his catatonic state. It turns out that the Kaiba that Yuugi is playing against is a Cyber Kaiba, controlled by the KaibaCorp computer, and using all of Kaiba's memories.

Yuugi defeats the "Automatic Giant" and Kaiba with a card called "The Unknown Egg."

(Source: Yu-Gi-Oh! Wikia)