I did check numerous times if Toho would allow something like this, and it looks as though, from my research (which provided very they few results, although I did find a few rewrite fics on TohoKingdom), that Toho wouldn't copyright strike this.
This story... took a while. I couldn't find a transcript on the internet, which no one is to blame for.
Also, because Zilla is a guardian monster in this, I decided to still keep the reference to a recent past film the same, but instead of Godzilla 1998, I decided to reference a different film, or rather different set of films.
Warning: Female Zilla! Doesn't go anywhere aside from a brief explanation about Zilla's history later on. You've been warned.
Our story begins with a briefing with the Japanese Self-Defence Force. Admiral Taizo Tachibana was explaining that "In the year 1954, a half century ago, our country suffered a terrible attack by Godzilla. Our capital was a battlefield. Only the courage of the men before us, saved this country from total destruction. That battle was the only battle our self-defence forces have had to fight since their foundation in that same year, 1954. Since then, our country has enjoyed a long period of prosperity. However, the peril has not disappeared. A few years ago, a three-headed monster attacked Hokkaido before being defeated. Since that attack, there have been numerous sightings in various countries..."
As he spoke, one of the recruits quietly muttered to another "That monster returned two years later, right?"
"That's what many people initially assumed it to be." the other recruit answered "Apparently they were only the same species."
"...The database is constantly being updated with new information." Tachibana continued before reading a message. "What's that..." he muttered before calling out "Dismissed."
He then left the briefing room as he puts on his marine captain's cap.
A new team is seen getting ready to cover the story. "An American nuclear submarine is missing off Guam in international waters." the reporter begins, "This morning, the navy set a search and rescue unit to help with efforts to locate the missing submarine and its crew members. Because of the potential nuclear risk, the navy is dispatching a rescue submersible called Satsuma. A navy cruiser with the Satsuma onboard will be leaving Yokosuka later today. Both vessels will be helping the Americans and their rescue efforts."
The Deep Sea Sub Satsuma was seen sailing through the ocean, with the rescue unit approaching the place the sub was last seen.
"Satsuma approaching search area." one is the pilots announced.
The pilots search and quickly found the submarine, which was in terrible shape. "There seems to have been an explosion." the pilot mutters. Just then, there is a sudden rumble, and very soon, a shadowy creature is seen approaching. Sand then covers the sea, obscuring the view of the ocean.
"I can't control it!" another pilot calls out. With little control, the submarine crashes into some rocks. "Hey, what's going on?!" the pilot asks before crashing and dying in the following explosion.
The other pilot watches as something blue glows across the rocks, swimming past them out of his line of sight.
"What's happening down there? What's that on the screen?" the person calling from the cruiser asks.
"I don't believe it!" the pilot yells, "It can't be happening!"