It could be Orochimaru. He has always been interested in dark and forbidden jutsus. He might have found a way to create the 'mob of the dead' situation to test his new powers or to capture Naruto for his own purposes. He could use his snake - like minions along with the undead to create chaos.
Kabuto Yakushi could also be the main villain. After his time with Orochimaru, he has amassed a great deal of knowledge about dark arts. He might create the 'mob of the dead' as a distraction while he tries to achieve his own goals, like stealing the secrets of the tailed beasts. He could control the undead with his medical - ninjutsu - turned - dark - magic and pose a serious threat to Naruto and his comrades.
One possible plot could be that the Naruto characters are trapped in a prison-like dimension similar to the mob of the dead setting. They have to fight against zombie - like creatures that are somehow related to dark chakra. Naruto could use his shadow clones to outwit the hordes, while Sasuke uses his Sharingan to detect the weaknesses of these strange foes.
It could be a new character, a powerful dark wizard who wants to use the combined power of Naruto's chakra and Pikachu's electricity for his own evil purposes. He creates all sorts of dark creatures and sends them after Naruto and Pikachu to try and capture them. He's very cunning and has a lot of minions to do his bidding.
A powerful demon named Malice could be the main villain. He has the ability to absorb both chakra and ki, making him a formidable foe for Naruto and Goku. He has a dark plan to destroy both the Naruto universe and the Dragonball Super universe and create his own realm of chaos.
Maybe a rogue ninja who has learned about modern technology and uses it to his advantage. He could be stealing valuable ninja artifacts and using modern gadgets to cover his tracks. He's smart like the villains in Case Closed, but also has the power of a ninja. He would be a difficult opponent for Naruto and Conan to face as he can blend the two different worlds' tactics.
A powerful dark wizard could be the main villain. He could be jealous of the clone's unique powers and want to steal them for himself. He might use dark magic to try and corrupt the clone or simply try to destroy it to prevent it from becoming too powerful.
Perhaps a powerful and unknown shinobi from a far - off land. This shinobi has heard of Team 7's reputation and sees them as a threat to his plans of world domination. He uses his unique and mysterious jutsu to challenge Team 7 at every turn, and they have to figure out his motives and weaknesses to stop him.
It could be a rogue Uchiha who has turned against the clan's values. He might be jealous of Naruto's power and popularity, and decides to use his Uchiha abilities to create chaos in the ninja world. He could also be trying to revive an old and dangerous Uchiha - related technique that was sealed away long ago.
It could be a rogue ninja who has a vendetta against Naruto and decides to target his son. Maybe this villain was once defeated by Naruto and now wants to take revenge by harming his family.
It could be a jealous relative who wants Naruto out of the picture so they can have more attention or power within the family.
Maybe a rogue scientist from the dead civilization who was experimenting with dangerous powers and was thought to be dead. But now he has returned with a vendetta against the living, seeing them as unworthy of the knowledge he believes is his.