People seem to forget without the 1998 film we wouldn't have Zilla Jr. or the animated series which was awesome. So instead of remaking the original 1998 movie I will do the canceled sequel:
Godzilla 2 (Unmade 1998 film sequel)
Dump the ENTIRE second script as well as Director Roland Emmerich and replace him with Jan De Bont, who was originally supposed to direct the first movie, and bring in Dean Devlin with Terry Rossio and Ted Eliott, who were originally supposed to write for the movie.
Base it in the Godzilla: The Series timeline, taking place just after "Monster Wars" with original actors from the first movie reprising their roles for the second movie along with new actors for Randy and Monique. Also make sure people know it's a live-action continuation of the TV series.
The new script would be an altered draft of the unreleased Godzilla (1994 film). The Movie would open with "Godzilla" {Zilla Jr.} fighting a giant mutant lobster in Maine. A nod to the Kaiju Ebirah and his debut film. After returning to New York and their HQ on Staten Island, Nick watches Zilla Jr. resting in his lair via a video feed. He expresses concern with how long he can keep the military and various world governments from attempting to take out "Godzilla". Elsie and the others try to cheer Nick up, except Monique because she's a French stick in the mud.
Meanwhile, somewhere in Kentucky, a meteor crashes into lake 'Apopka'. The "meteor" is actually an experimental weapon of the Tachyons that was sent to Earth to avenge their loss in the "Monster Wars" Mini series. In the original draft it was already of a hostile alien origin so it's easily changeable. With the Strange events occurring in lake Apopka, H.E.A.T. and the Military are called in to investigate. Audrey and Animal are also there covering the Meteor crash for their news station. In the lake, the Tachyion weapon starts to stir, flowing through the sediment like a mass of liquid metal. The probe enters a cave and absorbs a whole colony of bats along with a number of other life forms dwelling in the cave, creating probe bats and a number of other creatures. HEAT go in with the Military while Audrey and Animal sneak in past the military lines.
After meeting up the Probe Bats and other Probe creatures attack the party and carry off a number of red shirts/soldiers. Things are looking bad when Nick gets picked up by the Probe Bats, but suddenly Zilla Jr. comes bursting onto the scene and rescues him and the other humans killing off a number of the probe creatures in a large battle. Satisfied with the safety of everyone Zilla Jr. leaves and dives into the lake as the military scoops up the remains of the probe creatures and Nick and heat study them, discovering that these creatures were changed by Tachyon technology and the original probe is a more advanced alien version of the DNA creature from Trust No One.
Nick and Audrey have a romantic sub-plot during all this which continues to leave the audience guessing if they're relationship will make it through along with other various interactions between the human characters. Meanwhile the Probe Creatures which they continue to do battle with without Godzilla/Zilla Jr. continue to absorb animals, returning to the cave with their genetic collections to deliver to the main mass of the probe, which is slowly starting to take on a definitive form.
Nick and Monique put on diving suits and go to investigate where the meteor crashed with N.I.G.E.L. They discover a tunnel leading upwards from the bottom of the lake that leads them into a series of caves. Nick is shocked terrified when he sees a giant paw. The paw is attached to the newly formed shape the probe has assumed. It's the Gryphon which has the body and paws of a Puma, the arms and lower body of a human being, huge bat wings and a hydra-headed tongue composed of snakes In usual fashion kill off N.I.G.E.L., this time by being crushed by the giant hand like paws of the monster Nick and Monique try to flee but the Gryphon goes after them before it runs into Zilla Jr. {He's getting a lot more screen time then most Kaiju do in their movies.} After an underwater battle the Gryphon emerges and flies off with Junior in hot persuit. After determining it's course from satellite photos they determine that they're heading back to New York.
The Military try to kill it of course but in usual monster movie fashion nothing they try works on the monster. Causing people to die and buildings to be destroyed. However Nick with the help of the others manages to lure the Gryphon to the ruins of Madison Square Garden, so no one else can get hurt. There The Gryphon and Zilla Jr. Have their final battle. Using the same sort of special Harpoon they used on the DNA Mimic they fire the chemical at the monster which doesn't destroy it but it starts mutating into this horrible conglomerate blob of creatures and people it's absorbed which fires energy bullets everywhere. Zilla Jr. finally manages to destroy the creature with his Atomic Breath and after making sure there's nothing left of it leaves.
As the rest of New York is celebrating the demise of the Gryphon The Mayor of New York s rather upset another giant monster fight happened in the Big Apple. But thanks partially to Audrey's rather positive news report on the battle and Hicks telling the Mayor to count his blessings that the damages thanks to HEAT were minimal he shuts up about it. Nick also notes that they should expect more attempts at retribution by the Tachyons in the future. The scene then switches to the harbor and Zilla Jr. rises up from the water letting out a triumphant roar to a dramatically large full moon. In a post credits scene Monique is contacted by Philippe Roaché who informs her that he mutations are far more wide spread than they first believed and as he talks to her he faxes her a photo of the Japanese Godzilla from Godzilla 2000, saying this other Godzilla hasn't been seen since 1954. Linking the two films together in the same universe and setting up the next movie: Godzilla {Japanese} Vs. Godzilla{US}.