Fujin made his first chronological appearance in the spin-off game Mortal Kombat Mythologies: Sub Zero. He appeared here as one of the four guardians assigned by Raiden to protect Shinnok's amulet and was the first of the gods that Noob Saibot (by then the Elder Sub Zero) bested in order to acquire it (he is seen being torn asunder by his own tornado, but survived the ordeal).
He would remain inactive until the events of Mortal Kombat 4, being one of the few remaining Earthrealm gods not destroyed by Shinnok. He joined Raiden in his battle against his old enemy, assisting the Earthrealm forces in emerging victorious. After Shinnok's defeat, Fujin consulted with the Elder Gods. They revealed to him that he had a new task. Raiden appeared before him and informed him of his own impending ascension to the pantheon of Elder Gods. Knowing that the Earthrealm would need of a new protector, Raiden chose Fujin. Fujin accepted the position and promised Raiden that he would not fail him.
During the time of Mortal Kombat: Armageddon, Fujin became aware of a stark change in Raiden. He saw that the thunder god, while still seeking to protect Earthrealm, had grown to be ruthless. Raiden was now commanding the reanimated corpse of Liu Kang, who was killing many innocent people for unknown reasons. Fujin allied with Kung Lao in hopes that they could possibly find a way to save both Raiden and Liu Kang. From Kung Lao he learned of Johnny Cage's gathering of the Forces of Light and the mention of the brothers Taven and Daegon. It is revealed that Fujin had been a friend of their family for ages, and that he had questioned their father Argus when the two disappeared. He realizes that Argus placed them on a quest, but now this quest was becoming corrupted by evil. Fujin then goes to search for both brothers, hoping to prevent their progress and learn the true purpose of their quest.
Fujin reappears in Armageddon's Konquest mode, confronting Taven outside of the Red Dragon Clan's headquarters. He urges him not to enter, even if that means he will have to fight Taven to stop him. They do battle, but in the end Taven emerges victorious, allowing him to continue his journey but feeling regret at having had to do this to a friend.
In Fujin's Armageddon ending, after Blaze's essence flows into him, his powers grew immensely. Fujin then creates a new realm made from the ones destroyed by Shao Kahn. It would be the new place of origin for the forces of good. Fujin also assigns Kung Lao to be his new general.