Well, I'll go ahead and quote myself (with edits) about the situation and see if that'll work here.
"The nuclear explosion that mutated the Godzillasaurus did not just effect a single animal, but multiple (Godzilla 1954, Godzilla 2004, and one of the Showa incarnations, not sure which.) However only one of them attacked Tokyo in 1954. Sadly, the Godzilla that attacked Tokyo died (Godzilla 1954.) Shortly after though more Godzilla's began to surface!
One of them (Godzilla 2014, whom was actually a much more ancient relative of Godzillasaurus that was from the Permian) was attacked by the US Military after he awakened from a multi-hundred million year nap. Scared and confused at the time, he decided to go into a deep hibernation under the ocean.
Another Godzilla would eventually appear (Godzilla 2004), but this time it was located in Antarctica! This is where the aircraft the Gotengo battled with it, and thanks to a massive earthquake. This Godzilla got buried beneath the ice and he too fell into a deep hibernation.
This was then the time when the "last" Godzilla surfaced (the Showa Godzilla.) After his many years of being active and founding the Earth Defenders, he would later on have a son (Heisei Godzilla.) Showa Godzilla retired and went into retirement, while his son (Godzilla 1994) took his role as an Earth Defender.
Heisei Godzilla would once again take on the mantle of Godzilla and he too had not one, but two sons (Godzilla 2000 and Godzilla 2002.) It was around the year 1999 where Heisei Godzilla was attacked by the same ship that locked away Godzilla 2004 in Antarctica, and they tried the same tactic with Godzilla 1994 and successfully locked him away as well!
Leaving his two sons to wonder the earth by themselves, and they would eventually both take the mantle as Godzilla. However some unknown effect occurred where they both vanished. It is unknown what occurred to these two, but they most likely went into hibernation since the world was safe from invasions and enemies, and soon the Earth was Godzilla free.
Godzilla 2014 would make his return in the year 2014 and he became a destroyer of worlds and an Earth Defender! He too would have a son as well, but he is still young and growing.
Godzilla 1994 had also escaped his icy prison and returned! And soon his sons shall return as well. Godzilla 2004 shall also return and Showa Godzilla shall also come out of hiding."
More or less what I had in mind. I'm thinking Ghost Godzilla will be the reason why all the other Godzilla's return from their hiding/hibernation. Perhaps this could be the first big storyline?