The Martin Empire serves as the main antagonists of first half of the series' third season, though the group's creator went on to be the season's chief antagonist following the empire's downfall. This name is only used in the original version; the English dub does not give the group a name.
Following a personal tragedy, Professor Viper was sent on a mission to another country to research an unspecified target, but the plane he and his companions were traveling aboard crashed, with Viper emerging the only survivor. Nonetheless, he carried out his objective and was successful in locating his target–the severed hand of the Duel Monster Yubel–which entered into a pact with him to resurrect his son from the dead.
From the onset of the third year, Viper calls for an exhibition match between Jaden Yuki and Jesse Anderson at Duel Academy. Unbeknownst to the two combatants, they are fitted with special wristwatches known as Bio-Bands (Dis-Belts), designed to measure emotions, intensity, concentration, and decision making during Duels. Their true function, however, is to sap Duel Energy from those that wear them following the end of a Duel, regardless of whether one defeats his opponent or not. This gathered energy is then transferred to a chamber within Viper's hideout, the lab where Wheeler (SAL) was trained, to fuel Rick's revival.
To jumpstart his project, Viper declares that students of all dormitories must participate in Survival Duels (Dis-Duels), competitions wherein duelists are to carry Bio-Bands as means of assessing their fighting spirit. If a Bio-Band judges that a certain duelist lacks said fighting spirit, he or she will be demoted, and furthermore expelled if motivation does not improve. As a result of the Survival, a large number of students are injured and hospitalized after having their Duel Energy absorbed.
Eventually, Viper's intentions begin drawing concern from Academy staff, and Jaden and his friends set out to stop him. Tracking him to the laboratory in the jungle, the group is exposed to various sorts of traps and defenses installed to prevent its advance. Jaden would progress to confront and defeat Viper, though Yubel ultimately amassed enough strength to transport Duel Academy into an alternate dimension—a desert plane with three suns and resident Duel Monster spirits. Preying on the loneliness of Marcel Bonaparte, Yubel takes control of the boy's body and begins targeting the school's students and faculty, transforming many into zombie slaves to recruit more partners, and obtains the Sacred Beast Cards. However, Jesse Anderson succeeds in acquiring the Rainbow Dragon card and uses it to send the Academy and its students home, although he and Yubel remain behind.
During this time, Jaden and the Academy return to the dimension to search for Jesse and arrive in a different section of the dimension. While Jaden and the students battle the officers of the Dark World army, Jesse is possessed by Yubel. Intending to use Jesse as the avatar through which to secure the dimension in preparation for an evolution to a more powerful form, Yubel is opposed by Adrian Gecko, who challenges him for dominance even as Jaden rushes to challenge Yubel himself. Although Yubel was exhausted in a duel with Zane it had just previously had, it still defeated Adrian, and recovered its strength in the process. However, when Jaden finally duels Yubel to save Jesse, it is revealed that Yubel actually removed Jesse's soul from his body and placed him inside the Rainbow Dragon before taking over. Although Jaden manages to release Jesse, Yubel escapes and duels Jaden herself.
During Jaden and Yubel's duel, Syrus, demonstrating how much of a true friend to Jaden, follows suit after the two and on the way Syrus ends up talking to Chazz Princeton, who were apparently 'sacrificed' along with Alexis, Tyranno Hassleberry and Atticus. Chazz informs Syrus that when they disappeared in front of Jaden's eyes during a duel against Brron, the King of the Dark World, they were not killed, but transported to a different alternative dimension. The same thing had happened to Axel, Jim (who lost their duels against Jaden Yuki possessed by The Supreme King), Aster Phoenix (who lost his duel against Adrian Gecko) and Zane Truesdale (who lost his rematch against Jesse Anderson when he was possessed by Yubel).
During the final duel between Yubel and Jaden, Jaden understands that Yubel was a guardian spirit of Jaden when Jaden was apparently a prince of a kingdom. Yubel deciding to be the guardian of him transforms herself into the form that Jaden and the others see now. Syrus, who was watching the duel at the time, saw Jaden and Yubel disappear into what was the center of the 12 dimensions. But before Jaden disappeared, Jaden did his signature pose and promised that he would finish the duel and return when he 'became a man'. In the center of the dimensions Yubel activates a trap card that would allow her to destroy all the dimensions at once and Jaden at the same time. But Jaden, after realizing that Yubel was doing all this to protect him, uses Super Fusion to fuse not the monsters that Jaden and Yubel had on the field, but to fuse Jaden and Yubel souls together in order to 'become one'. The duel supposedly ended in a draw and after this, most of the students who accompanied Jaden to the other dimension arrive back in the real world. Zane, Adrian, Bastion and Jaden do not return when the gang came back and are presumed 'missing'. However, prior to Jaden's final duel with Yubel, Bastion decides to remain as a denizen of the alternate dimension with Tania and her friends.
The following day, Syrus and the rest of the gang discuss the proud moments when they met Jaden, but Chazz gets reminded on how much he hated Jaden for beating him. As this was happening, Syrus ran off into the forest and remembered the scene of which got his last view of Jaden. But just at that moment, in which he wished for Jaden to return, a shooting star crashes onto Duel Academy island in which the star was actually Jaden returning. With Jaden returned Syrus ran up to him and in which the season comes to an end. After Yubel's defeat, Zane is found unconscious on Duel Academy's shores in the fourth season and is then brought to the infirmary to recuperate. Adrian's whereabouts are currently unknown.
- Yubel - A psychopathic Duel Spirit, Yubel serves as the unquestioned leader and mastermind of the whole organization.
- Marcel Bonaparte - As the puppet leader of the official Martin Empire, Yubel uses him as a medium for the others to do its will.
- Professor Viper - A grieving father bent on saving his son, Viper is Yubel's top subordinate before the formation of the official Martin Empire.
- Titan, the Rock Spirit - A Duel Monster Spirit which was summoned by the Yubel-possessed Marcel Bonaparte.
- Three Masked Knights - Three students seduced by power and forcibly bonded to three Duel Spirits, the Three Masked Knights are Yubel's unwilling pawns.
- Duel Ghouls - Most of the Duel Academy students controlled by Yubel's power, they serve as Yubel's mindless drones.
- Adrian Gecko - Joined Yubel briefly so that he may use her power to unleash Exodia.
- Jesse Anderson - Became Yubel's newest host after sacrificing himself to bring Duel Academy back to its dimension.
Before the Martin Empire was formed Viper had several duelist to try and gain enough energy for Yubel.
- Axel Brodie - Was Professor Viper's protégé until Axel found out about the Bio-Bands draining energy.
- Mr. Stein - A former pro-duelist who blames Jaden for the student's behavior at Duel Academy
- Trapper - A man who can see duel spirits and catches them for their energy.