Over 1,000 years ago, Haxorus served Jaden, who in turn served Arisia, the godess of Kamerai Palace. Haxorus was sensitive to a pink aura. Haxorus could use a pink aura as an offensive attack in the form of Psystrike (Mewtwo's signature move), in which he would make mysterious brain waves real and attack the opponent. Jaden taught Haxorus how to refine his sensitivity to a pink aura.
When Kamerai Palace was about to be caught in the middle of a war, Jaden was on his way to the Stone of Time to attempt to stop the battle when he came across Haxorus, who had been temporarily blinded by a group of sand-kicking Linoone, where Jaden told him that he was never going back to the castle. Jaden intended to sacrifice himself to stop the war, but Haxorus jumped to the conclusion that he was abandoning the kingdom, which caused Jaden to throw his staff, sealing Haxorus within. The armies raged past the staff, and Jaden's Skarmory later returned it to Arisia. After sealing Haxorus, Jaden sacrificed himself to the Stone of Time to stop the war, and he succeeded.
Years later, in the present time, Haxorus was awoken from the staff when it was held by Lucas, who has a similar aura pattern to Jaden. Still blinded from the attack years ago, Haxorus initially mistook Lucas for Jaden, but he regained his sight, but was stubborn and distrustful of humans after being sealed in the staff. Unaware of Jaden's sacrifice, Haxorus held a grudge toward Jaden, thinking Jaden had abandoned the castle and him. He had considered himself Jaden's servant, and he could not understand the friendship between Lucas and Monferno. However, a Mirage Flower message left by Jaden shortly before his death told Haxorus the truth, that Jaden considered Haxorus a friend, not a servant.
Once again the Stone of Time was disturbed, threatening to destroy the balance between Pokémon and nature. Lucas and Haxorus rushed to its core and began to use their psychic powers to energize the stone's defense system. Using up their pink aura would have meant the same fate as Jaden: death. However, just as Lucas was about to use up his aura and give his own life, Haxorus pushed him away, instead sacrificing only himself to the stone.
After Haxorus's death, the portrait of Jaden in Kamerai Palace was altered to include Haxorus by Jaden's side, cementing their relationship as best friends and partners in psychic manipulation. Haxorus is later seen with Jaden once again and gives him a bar of chocolate, which he enjoys; this is surely after his death, as Haxorus did not know what chocolate was until Barry gave it to him in an effort to earn his trust for the sake of the group.
Haxorus is the second Pokémon to perish and not be revived in the comic, the first being Giratina.
Haxorus states that he is the real legendary Pokémon, though he is explicitly a pseudo-legendary in the games.
In the Super Jump Punch! Issue #19, Arkeis, or "Aragonbird", incorrectly states that Haxorus can talk due to it being a Dragon/Psychic Pokémon. Haxorus is actually a pure Dragon-type, while his ability to talk was given by the pink aura.
Haxorus was shown to learn Psystrike, as Haxorus can't legitimately learned this move in games.