Bitter over the loss, Kaiba plots an elaborate revenge. He successfully acquires the other three Blue-Eyes White Dragon cards in existence and builds "Death T," a "theme park" comprised of many deadly games and challenges designed to end the lives of Yugi and his friends. After being subjected to the hazards, Yugi and his friends witness a Duel Monsters match between Seto and Yugi's grandfather, who was forced to participate when Kaiba threatens Yugi's life. Kaiba wins and tears up Sugoroku's Blue-Eyes White Dragon. Kaiba then challenges Yugi to an immediate rematch. Although Kaiba proves formidable with the three Blue-Eyes in his deck, Yugi ultimately wins by forming Exodia. Yugi then uses the power of his Millennium Puzzle to subject Kaiba to a Mind Crush, shattering his mind to pieces and leaving Kaiba comatose. Kaiba eventually regains consciousness later in the manga during the Duelist Kingdom arc.
In the second series anime and its adaptation of the manga, Kaiba instead kidnaps Sugoroku and duels him to win the card. Kaiba already owns the other Blue-Eyes at this point, and acquires the fourth card to destroy it so nobody could use it against him. To avenge his grandfather, Yugi duels Kaiba and defeats him with Exodia, then uses his powers to purge the darkness that has clouded Kaiba's mind. Kaiba subsequently loses interest in dueling and his company and leaves on a trip to find himself. In both the anime and manga, with Kaiba gone, Duel Monsters creator Maximillion Pegasus schemes to take control of Kaiba Corp from Seto by conspiring with its board of directors, the Big Five, and abducting Mokuba. Part of his plan involves hosting a Duel Monsters tournament on his private island, Duelist Kingdom, which Yugi participates in.
In Season Two of the anime, Kaiba is summoned to the Domino City museum by Egyptologist Ishizu Ishtar, Kaiba is shown the ancient stone tablet that depicts the duel between his past self and the Pharaoh. Although Kaiba does not believe into Ishizu's warning that history was sure to repeat itself, he is greatly interested by her tale of the Egyptian God Cards - three massively powerful one-of-a-kind Duel Monsters cards that Pegasus has entrusted to her. Two, however, were already stolen by her brother Marik, and she gives the third - Obelisk the Tormentor - to Kaiba, encouraging him to hold a tournament of his own to draw in Marik and his organization, the Rare Hunters. Seeking to obtain the remaining two God Cards for himself, Kaiba agrees, and begins his "Battle City" tournament, which Yugi and Joey Wheeler become participants in. During the tournament, Kaiba easily defeats his opponents using Obelisk the Tormentor while Yugi wins his own God card, Slifer the Sky Dragon. Eventually, Kaiba reluctantly teams up with Yugi to rescue Mokuba and Yugi's friends from Marik. Afterwards, Yugi, Kaiba and Joey enter the finals, unaware that Marik has made a deal with Yami Bakura, and he, along with Marik and Marik's stepbrother Rishad, are registered as well. During his duel in the finals, Kaiba duels Ishizu herself. After receiving a vision from Marik's Millennium Rod, the same Millennium Item his past self owned, Kaiba forgoes his originally desired strategy of using Obelisk the Tormentor to defeat her and sacrifices it to summon the Blue-Eyes White Dragon, which, obviously was his past-life's monster in the duel against the Pharaoh. With the White Dragon, Kaiba manages to trump Ishizu's prophecy of defeat and claim victory.
In Season Three, Kaiba faces Yugi in the semifinals, and the two unleash their Egyptian God cards against the other. When the two finally attack each other, they each receive a vision of their past selves dueling. Encouraged by the vision, Yugi manages to defeat Kaiba and go on to the final battle against Marik. Although initially disgusted over his loss and determined to blow up the island the duel is being held on, Kaiba is convinced by Ishizu to stay and watch the battle between Yugi and Marik. Kaiba gives Yugi the card Fiend Sanctuary prior to the duel, and with it, Yugi is able to hold off the attacks of Marik's Winged Dragon of Ra and defeat him. The entire group narrowly escapes the island before it explodes afterwards.
Shortly after his return from the Duelist Kingdom, the Big Five attempt to placate an outraged Kaiba by revealing that they have finalized his virtual reality game software, and invite him to test it out for himself. However, this was merely another attempt to do away with Kaiba, but Yugi and his friends manage to rescue him. The Big Five log into the virtual world in an attempt to stop them from escaping, but they are defeated in a duel, and their own minds became trapped in the virtual reality program. Some time later, in the midst of the Battle City tournament, the Big Five's digital consciousnesses are discovered stranded in cyberspace by a mysterious boy named Noah, who recruits them for a revenge campaign against Kaiba. The craft taking the Battle City duelists to KaibaCorp Island for the finals is hijacked by Noah, who then traps Kaiba, Yugi and several of Yugi's friends in his own rendering of the virtual world, forcing them to duel the Big Five.
As Yugi and his friends defeat the Big Five, Kaiba's past is revealed (see above), and Noah ultimately admits to being Gozaburo Kaiba's biological son, and claims his mind exists as a computer program after he was fatally wounded as a child and subsequently digitized. Although Kaiba ignores Noah's claims and duels him, Mokuba is more sympathetic as Noah's blighting by Gozaburo, who began to neglect Noah and breed Kaiba as his new heir. After Noah is defeated, Gozaburo reveals himself as alive and inside the virtual world, and sets a series of orbital missiles to launch and destroy the world. While Kaiba stops Gozaburo, a reformed Noah sets the base on which the virtual world software is held to selfdestruct, and helps Yugi and his friends escape. Afterwards, the anime continues on to the Battle City finals.
In Season 4 of the anime, Kaiba, along with Joey and Yugi, is one of three duelists chosen to fight the Atlantean King Dartz. During the season, Kaiba meets Alister, an orphan whose brother and parents were killed by KaibaCorp owned military forces under Gozaburo Kaiba's command. Due to his love for his brother, Kaiba becomes sympathetic to Alister and carries his soul-less body to safety after their duel. Kaiba and Yugi eventually duel Dartz, and although Kaiba loses, Yugi defeats Dartz and Kaiba is restored and takes part in the battle against the Leviathan.
In the first half of Season 5, KaibaCorp's stock prices are at an all-time low as a result of a failed takeover by Dartz, and when Kaiba hosts a tournament to restore the company's reputation, Zigfried von Schroeder infiltrates it and hacks Kaiba's computer systems. Catching Zigfried, Kaiba quickly dispatches him a duel. However, Zigfried has his brother Leon duel Yugi in the finals. During the duel, Zigfried tricks Leon into activating Golden Castle of Stromberg, releasing a computer virus into Kaiba's system and forcing Leon to attack and thus forcing his hand. However, Yugi prevails while Kaiba, who anticipating such a plan, has already had his computer systems backed up.
Kaiba proceeded to challenge Yugi to yet another duel in his Duel Dome, and put the first of the two cards into play - the enigmatic "Pyramid of Light," which prevented the Egyptian God Cards from participating in the battle. As the duel proceeded, however, it was revealed that Kaiba had been used as a puppet for the ancient Egyptian sorcerer, Anubis, who had placed the Pyramid of Light card in Pegasus's deck. The Pyramid's powers were draining the lifeforces of Yugi and Kaiba as the duel progressed, eventually resurrecting Anubis, who dispatched Kaiba and took his place in the duel. With Kaiba's aid, however, Yugi put the second mighty card into play - the Blue-Eyes Shining Dragon, able to destroy any card in play. The Shining Dragon destroyed the Pyramid of Light, and subsequently wiped out Anubis.
Throughout the anime, Kaiba's role in the events of the past are constantly hinted, but not explained it detail. In the fifth season of the anime, Kaiba is revealed to be the reincarnation of the ancient Egyptian priest Seth (named for the Egyptian deity Set), cousin to the pharaoh Atem, whose spirit inhabits the body of Yugi Mutou in the present day. Holder of the Millennium Rod, Seth was one of the most dedicated followers of the pharaoh, but his father, Akhenaden, hoped that one day, Seth would rule Egypt. When the Pharaoh came under threat from Thief King Bakura, Seth had many villagers gathered together that he might identify those with powerful "Ka" - monsters created by the power of their souls - that might help to defend the Pharaoh's rule. This act, however, was performed without the Pharaoh's knowledge, as was the decision to have the prisoners fight to the death to strengthen their Ka and find the single most powerful one. One of the prisoners was a girl named Kisara, whose Ka was the Blue-Eyes White Dragon. Subsequently, when Akhenaden was empowered by the demon Zorc Necrophades, he killed Kisara and extracted her Ka. When Zorc was then defeated by the Pharaoh, Akhenaden committed suicide and his spirit possessed Seth, forcing him into a duel with the Pharaoh, during which he called on the power of the Blue-Eyes White Dragon. Seth was poised to win, but Kisara's spirit was able to purge Akhenaden from Seth's mind; the pharaoh went on to sacrifice himself to seal away the magic of the Millennium Items, and appointed Seth as his successor. Their duel, however, was forever preserved on a massive stone tablet depicting the two combatants.
Although magical powers and items are often employed in the series, as a rational man, Kaiba does not believe in such things, and, when necessary, convinces himself that it is all tricks and illusion. Although this trend had a tendency to be exaggerated in the English version of the series, it is present in both language versions of the anime and manga. Eventually he grudgingly comes to accept that there is little other explanation for the bizarre, fantastical events he witnesses throughout the series. In a similar vein, Kaiba is shown to have an affinity for machines and as such manufactures several holographic devices for Duel Monsters, and as suggested by Tea Gardner in the English dubbed anime, this may be the cause of his misanthropy.
Kaiba changes in personality from the second season of the second series anime onwards. In the first season, Kaiba acknowledges Pegasus' ability to read minds, as well as the "Heart of the Cards". Although he does not like Yugi and Joey, he does not act outright hostile towards them, except during the first episode. However, in the second season, his acceptance of faith and magic vanishes and, in the English anime, he adopts the habit of saying that it's "hocus-pocus nonsense". His desire to defeat Yugi also grows from a grudge to an obsession, and Kaiba shows an outright disregard for the safety of Yugi and his friends. Despite this, he still often helps them with defeating the villains they face, usually claiming that Yugi or one of his friends helped him and he thus owes them, or that the villain's desires are in direct conflict with his own interests.
Kaiba's only appearance in person comes when Sartorius visits him to request the use of his Kaiba Land amusement park. Kaiba's character design in Yu-Gi-Oh! GX is identical to his original appearance, although his facial structure is changed subtly. Due to the fact he is nearly thirty years old, Sartorius makes an inside joke about his teenage appearance. Kaiba indicates he knows about the Society of Light, although such knowledge is not expanded upon. Kaiba has not made any other appearance since, though it has been shown that he is the only surviving citizen of Trueman's invasion in Domino City.
Kaiba also appears in all of the Yu-Gi-Oh! related video games as an opponent which the player can duel.
Kaiba's signature cards are his three Blue-Eyes White Dragons and the fusion monster formed from the three dragons, the Blue Eyes Ultimate Dragon. At multiple times, he has shown the ability to draw the beast whenever needed, and sometimes even draws all three at once. Summoning a Blue-Eyes for a final assault is Kaiba's trademark victory move. To this end, he also utilizes a wide variety of support cards to power up the Blue-Eyes and make it easier to summon. However, he does utilize other cards in his deck.
Kaiba's deck all-around relies on a beatdown strategy of overwhelming an opponent with powerful monsters. Early on his deck is composed of Beast, Fiend and Beast-Warrior monsters, all of which are mentioned by Maximillion Pegasus at one point to have more than 1500 ATK points save for Saggi the Dark Clown. At this time Kaiba also becomes notorious for his Crush Card, a card that destroys all of an opponent's monsters with an ATK above 1500 points (During the "Waking the Dragons" arc, he fused this card with the Legendary Dragon he freed in his dream, creating the Doom Virus Dragon). Combined with his own assortment of high-powered monsters, such a move all but ensures Kaiba's victory.
During Battle City, Kaiba uses a deck focusing more on Machines, especially Cyber Jar and the XYZ series. After Battle City, Kaiba's deck features more Dragon-type cards to compliment his Blue-Eyes, including Thunder Dragon and Spear Dragon. He eventually adapts to a Dimension strategy of removing his cards from play, then returning them with Dimension Fusion/Return From the Different Dimension for a final assault. However, his Blue-Eyes still serves as his trump card.
In Yu-Gi-Oh! GX, Kaibaman's deck, based on Kaiba's own, focuses on summoning and protecting the Blue-Eyes White Dragon.