Origin: The Heavens
Fujin first appeared in Mortal Kombat Mythologies: Sub Zero as one of the guardians of Shinnok. There he was defeated in combat by Noob Saibot, barely surviving the ordeal. At the beginning of Mortal Kombat 4, Fujin joins Raiden as one of the few surviving Earthrealm gods to fight against Shinnok's force invading Edenia. After emerging victorious from the battle and defeating Shinnok, Raiden is chosen to be made a new Elder God and must name a successor to protect Earthrealm. He chooses Fujin, who continued to protect Earthrealm up to the events of Mortal Kombat: Armageddon.
Raiden began to act oddly during the course of Mortal Kombat: Armageddon. Fujin became concerned. Though Raiden was still trying to protect Earthrealm, Fujin saw his actions as unnecessary and needless, especially bringing Liu Kang back from the dead as a warrior. Fujin turned to Kung Lao for help in saving Raiden, and from him learned of Taven and Daegon's role in stopping Blaze and Armageddon. A friend of their family and sensing something has gone wrong, Fujin set out to find the two brothers to find out what is going on.
After defeating Shinnok, Raiden appoints Fujin as Earthrealms new protector to replace him as he ascends to the rank of Elder God.
Shortly after Blaze's defeat, Fujin becomes incredibly powerful. Using this power he creates a new realm to serve as a place for the forces of good from the pieces of all the realms that Shao Kahn has destroyed or ravaged. He then appoints Kung Lao as his general.
Fujin appears in Kratos' ladder ending alongside Raiden. The two gods bow to Kratos in respect for his defeat of Shao Kahn.
Mortal Kombat X
Fujin makes a minor appearance in the game fighting alongside Raiden.