There could be some vengeful ex - employees of Mokuba's family business. They feel that they were wronged by the family in some way, and they think that kidnapping Mokuba is the best way to get revenge. They might have planned the kidnapping carefully, waiting for the right moment to strike.
Maybe it's a group of thieves who heard that Mokuba comes from a wealthy family. They believe that they can get a huge ransom for his return. So they target him and try to snatch him away when he is alone or unguarded.
It could be some rival businesspeople who want to use Mokuba as a bargaining chip against his family's company. They might be jealous of the power and success of Mokuba's family and think that by kidnapping him, they can gain an upper hand in the business world.
Anzu may physically defend Mokuba if it comes to it. She could use self - defense moves she has learned. If the kidnappers get too close to Mokuba, she jumps in front of him and uses her strength and agility to fend them off. She might also use nearby objects as weapons, like a stick or a rock, to keep the kidnappers at bay.
Maybe there are powerful dark sorcerers. These sorcerers could be trying to capture Naruto for their own evil purposes, like using his power to open a portal to a dark dimension or something, and Kurama has to protect him from them.
Maybe some of Tony's business rivals who have access to advanced technology. They could be jealous of Tony's relationship with Ultron and try to harm him. They might hire mercenaries or develop their own weapons to go after Tony. In this fanfiction, these rivals would be the main antagonists as they constantly try to break through Ultron's protection of Tony.
In many cases, the main antagonists can be other Slytherins who still hold grudges against Harry or are loyal to the pure - blood supremacist ideology. They might see Harry as a threat to their way of life. Also, some Death Eaters can be antagonists. They target Harry because of his role in Voldemort's downfall and would stop at nothing to get to him.
Perhaps there are some shinobi within the village who are jealous of Naruto's potential. They might try to harm Naruto in secret, and Hiruzen has to be vigilant against them. These shinobi could be from clans that have rivalries with the Uzumaki or those who just don't want a new powerful force emerging in the village.
It could be the Fire Nation remnants who still hold grudges against the airbenders. They might be trying to finish what they started years ago.
Some fanfictions might introduce new original antagonists. These could be powerful rogue ninjas who are after Sakura for her medical skills or some special power she might have in that particular fanfiction. They would then be the main threats that Itachi has to deal with to protect her.
Another possibility is a new and powerful enemy from a neighboring village. This enemy might view fem Naruto as a symbol of the strength of her village and wants to take her out to weaken the village. Shikamaru then has to protect her from this external threat.
It could be Orochimaru. He's always been after power and Naruto's unique abilities would be very appealing to him. So the fem Kyuubi would have to constantly be on guard against Orochimaru's schemes.
In some fanfictions, there could be other dark wizards or witches who are allied with Voldemort or have their own reasons for wanting to harm Harry. Snape would have to protect Harry from these various threats as well. For example, some Death Eaters might try to take matters into their own hands and go after Harry without Voldemort's direct orders.