It could also be a corrupted version of Baldur himself. Maybe the crossover has some unforeseen side effects that twist Baldur's mind. He becomes more power - hungry and cruel, seeing Kratos and Atreus as obstacles to his new - found goals. Kratos then has to not only deal with this new threat but also try to find a way to save Baldur from himself.
Odin could be the main antagonist. He is a powerful and manipulative figure in Norse mythology. He might see Kratos as a threat to his power and send Baldur to deal with him. But in reality, Odin could be using both of them for his own dark purposes, like obtaining some powerful artifact or spreading chaos in the realms.
A plot could involve Baldur being sent to the realm of God of War by Odin to spy on Kratos. However, Baldur is intrigued by Kratos' strength and his relationship with his son, Atreus. Baldur starts to question his own loyalty to Odin. Meanwhile, Kratos is suspicious of Baldur but also sees a bit of his own past self in Baldur's blind obedience to a cruel father figure. Eventually, they work together to resist Odin's control over Baldur.
Zeus could still be a main antagonist. After all, he was a major foe in the original games. He might be even more vengeful in the fanfiction, seeking to completely destroy Kratos for his past insurrections.
It could be an ancient evil that has been awakened by the chaos of the two universes colliding. This entity is powerful and has the ability to manipulate the very fabric of the Gears of War and Ben Carmine's world. It wants to destroy both worlds and reshape them in its own dark image, and Ben Carmine and the Gears have to figure out a way to stop it before it's too late.
It could be another powerful mage who is jealous of Natsu's new war god slayer magic and wants to steal it for himself. This mage might have been researching ways to gain such powerful magic for a long time and sees Natsu as an obstacle to his own plans.
A new antagonist could be an ancient and powerful sorcerer. This sorcerer has been locked away for centuries but has now broken free. He wants to take over the realms and sees Kratos as a major obstacle. He has the ability to control the elements in ways that Kratos has not faced before, like creating huge tsunamis or summoning volcanic eruptions.
Orochimaru might also be a main antagonist. He is always after power and knowledge. In the context of the 4th war with a god involved, he could see the god as a source of ultimate power. So he might try to manipulate the situation to either steal the god's power or use Naruto to get to the god's power. He could be secretly working behind the scenes, causing trouble for Naruto and his allies.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
A powerful demon from another dimension could be the main antagonist. This demon could be attracted to the power that Sinbad wields in the Magi world and wants to steal it for himself. He could start causing chaos in both the world Sinbad is from and the world he's been transported to in the crossover.
A new character could be introduced as the main antagonist. For example, a being from another dimension who has been observing both Sonic's and Megaman's worlds. This being realizes that by combining the chaos energy from Sonic's world and the advanced robotics technology from Megaman's world, it can create a new, all - powerful empire. So it starts to manipulate events in both worlds to bring about this combination, while Sonic and Megaman have to stop it.
Dr. Eggman and Dr. Wily could team up. Dr. Eggman has his mechanical creations and knowledge of Sonic's world, while Dr. Wily is an expert in creating powerful robots in Mega Man's world. Together, they could be a formidable force against Sonic and Mega Man.