Perhaps a new, even more powerful Locust - like creature could be created specifically to counter Goku. This new antagonist would have some unique abilities that would pose a challenge even for Goku's super powers. It could be a genetically - enhanced Locust with the ability to absorb Ki or something similar.
The Locust Queen could still be the main antagonist. Goku would see her as a great threat to the people of Sera. His sense of justice would drive him to take her on directly.
It could also be a human traitor within the COG. Goku would be so focused on the external threats like the Locusts that he might not initially suspect a human as the main antagonist. This traitor could be working with the Locusts in some way, and Goku would have to use his detective skills (which he might not be so good at initially) along with his combat skills to expose and defeat this hidden enemy.
It could be really exciting. Goku's super strength and combat skills would be a great addition to the Gears of War universe. He could use his Ki blasts against the Locust horde, and his ability to fly would give him an edge in battles. Maybe he'd team up with Marcus Fenix and they'd take on the toughest enemies together.
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 Zamasu. Since Goku Black was Zamasu in Goku's body in the original story, perhaps a more powerful and enraged Zamasu could be the main antagonist. He might be jealous of the new fused form's power and seek to destroy it.
Maybe an old enemy of Goku's who has somehow managed to return. This enemy has heard about Goku Jr and figures that by attacking him, he can get revenge on Goku. This could be someone like Frieza who has found a new way to be resurrected and is more powerful than ever.
I'm not sure who 'Master Cheff' specifically is in Gears of War fanfiction as it could be a unique character created by a particular fan writer. It might be a chef - like character with some special skills or role within the fan - created story set in the Gears of War universe.
Maybe an interdimensional warlord who sees Goku as a threat to his conquest plans and Lemon as a valuable asset. He would stop at nothing to capture them and gain their powers. He could have an army of minions from different dimensions, making it really challenging for Goku and Lemon to fight back. This antagonist would be very cunning, constantly devising new strategies to outwit our heroes.
Maybe it's a new character created specifically for the fanfiction. This character could be a powerful sorcerer who has the ability to manipulate people's minds. He targets Goku out of jealousy for his power and popularity. By using his mind - control powers, he makes everyone around Goku believe that he's a traitor, thus making himself the main antagonist.
It could be someone like Madara Uchiha. He's extremely powerful and his goals are often in conflict with Naruto's. Goku would have to face his Sharingan abilities and his vast array of jutsu.
Frieza would be a great antagonist. If Goku goes back in time to a point before Frieza was defeated, Frieza could be an even more menacing force as Goku might not have all the power - ups he had in the original timeline. He'd have to rely on his wits and basic training more.
There's also the possibility that Orochimaru could be the main antagonist again. He might be intrigued by Naruto's new powers and try to experiment on him. Orochimaru is always after power and knowledge, and Naruto's Saiyan powers would be something he'd be very interested in. He could use his snake - like abilities and various jutsus to try and capture Naruto.