I'll go ahead and theorize as to what his story will be by making up my own right here. Who knows, maybe I'll be right.

Story:

Nightwolf, one of Earth's great chosen warriors durnig the conflict with Shao Kahn, has returned to defend the Earth once more at Fujin's request. Having been a powerful ally in the past, Nightwolf's shamanistic powers had preserved and protected his lands during Kahn's invasion, and with his ancient magics, Nightwolf poses a formidable threat to the Dragon King and his invading forces.

Having spent the last several years preserving the culture of his people, Nightwolf had not been in contact with his former allies. Saddened to hear of the loss of his former friend and ally Liu Kang, Nightwolf has vowed to defend Earth in his stead, even if it costs him his life. The enemies of Earthrealm will find Nightwolf to be a most dangerous adversary.

That is a really good story and I would definitely put my money on you being right. I guess Nightwolf is thinking that Kang didn't find his animality at this point since Liu Kang is dead lol.

I've two theories about his return:

1) Many Earthrealm warriors are dead, and Raiden had to ask Nightwolf to join him since he had no warriors alive to command against the Dragon King.

Remember, in Konquest (MKDA) it was said that Raiden asked many warriors to join him against the Deadly Alliance, and a few went to Shang's island. Nightwolf might have been one of those warriors, but sensing the menace of the Alliance, he didn't want to leave his sacred land to protect it if the sorcerers were succesful.

2) While classic Earthrealm warriors (Jax, Sonya, Kung Lao, Cage, Cyrax) are fighting against the Red Dragon (or another evil menace) on Earth, another group of warriors (Nightwolf, Sub-Zero, Kenshi, Raiden, maybe Scorpion...) went to the Outworld to battle the Dragon King...

And that would explain why we haven't seen yet Jax, Sonya, Kung Lao, Cage, Cyrax... etc