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The book would have kaiju pre-existing already in the Evangelion universe, but almost every kaiju besides Godzilla Junior, would go missing after the second impact.
The prologue of the book would include Godzilla Senior (with the Heisei Godzilla body) in his burning form, Junior and Jet Jaguar converging onto Adam. Every other kaiju would be either on Monster Island, or rushing to assist Godzilla. As the Second Impact was beginning, Senior would go into meltdown. Jet would try and take away Junior, but he refused to leave his father. As both Kaiju and Angel detonated, Junior, and every Kaiju on Earth would get buried and sealed away.
Senior would have died in the prologue, but his meltdown and detonation would have not done anything to the planet. It would have done a huge number on the Antarctic, but due to Adam's Second Impact, the heat would have been held back from hitting anywhere else in the world. The radiation would have all been absorbed by Junior, which would accelerate his growth into his own adult body, which would be the 2002/Matt Frank Godzilla design.
Due to being buried so deep, all of the kaiju would also end up being undetected from NERV's scanners. Eventually, during Shinji's first battle, Junior would wake up by pure chance and detect the presence of the angel. Remembering the death of his father and seeing the damage it did to the planet, Junior fueled himself with newfound anger, which only increased when he realised the angel was already in a city, which struck Junior's soft spot for humankind.
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Later on, Junior would show up after the first few angels were beaten, revealing his presence once more to the world. The majority would be shocked, Shinji would pray to whatever God was out there that he'd never have to fight Junior, Asuka would do the opposite, Misato would get flashbacks to Antarctica and Gendo would get mad.
As the story would progress, more Godzilla allies and enemies would appear. Skull Island would be the only thing really unaffected by the Second Impact, due to the version I intended to use being the Monsterverse version, and so the storm would have protected the island and it's waters. Kong and every kaiju on Skull Island would still be there undisturbed, but due to NERV not being able to properly reach the island itself, they had no way of confirming if the kaiju were still there or not.
I would have also included some other things, such as maybe making Maya Ibuki the daughter of Jet Jaguar's creator: Goro Ibuki ('cause y'know, same surnames and all. How can I pass up an opportunity like that?) and basically, Maya would be the only one who'd be really happy that Junior was alive. Jet would have reappeared during the Jet Alone fiasco.
Another thing that'd happen would be at some point Gendo would try and kill Godzilla by the orders of SEELE, which would lead to Junior decimating basically everything NERV had. When the obligatory Godzilla vs Eva fight would happen, Junior would take down Rei and Asuka first.
