There could be an ancient evil entity that has been awakened by Godzilla's presence. This entity wants to destroy everything in its path and sees Godzilla and Izuku as obstacles. It has the power to corrupt other creatures and turn them against our heroes, making it a very formidable antagonist.
Maybe it's Obadiah Stane. He's jealous of Iron Man's success and with Izuku in the picture, he sees an opportunity to get rid of Iron Man once and for all. He could also see Izuku's quirk as something he can use to his advantage, so he tries to capture Izuku and use his power against Iron Man.
Another possibility is that in the world where Goku Black comes from, there is an enemy who follows Goku Black to Izuku's world. This enemy could be a powerful Saiyan or a being with a dark ki similar to Goku Black. They might see Izuku as a weakness in Goku Black's plan and try to eliminate him first, making them the main antagonist in the fanfiction.
One possible plot could be that Izuku, while on a training mission in an uninhabited area, stumbles upon Godzilla. At first, he's terrified but then realizes Godzilla doesn't seem to be immediately hostile. Izuku tries to communicate using his knowledge of quirks and signals. Godzilla, in turn, seems to recognize Izuku's heroic nature and they form an unlikely alliance to protect the area from a common threat, like a group of villains who want to use Godzilla's power for evil.
It could be Hydra. They might be trying to take advantage of the split between the Avengers and the Rogue Avengers. They see Peter as a wild card and try to either capture or turn him against both groups.
Well, it could be Dracula himself at first. Since he is a vampire and has a rather menacing reputation, he might be seen as the antagonist. He could be trying to do things that are not so friendly towards Alvin and the chipmunks, like scaring them or having some sort of plan against them.
Maybe there's a villain group that targets Izuku specifically because of his money. They want to steal his wealth to fund their evil schemes. They might try to kidnap him or hack into his financial accounts. Izuku then has to use his wits as well as his money to outsmart them.
Lex Luthor could be a great main antagonist. He might see Izuku as a threat to his plans, especially if Izuku's unique abilities and sense of justice start to disrupt Luthor's schemes in the combined universe. Luthor could try to manipulate events to turn the Justice League against Izuku or find a way to steal Izuku's power for himself.
Obviously, Dracula would be the main antagonist. He is a vampire, after all, and his nature is to be somewhat menacing. He has powers like turning into a bat, hypnotizing, and super strength. All these things could pose a threat to Alvin and the Chipmunks.
In this fanfic, the main antagonist could be a scientist who has been corrupted by his own experiments. He creates some sort of energy - based monsters that are immune to normal attacks. Captain Marvel and the Avengers have to figure out how to stop these creatures and the mad scientist behind them.
A powerful sorcerer who wants to steal Izuku's Unlimited Blade Works power for his own evil purposes. He could be from a hidden world of magic and have minions that Izuku has to fight through.