Hiroshima 1944, we see a Japanese guy playing with a pocket watch in a helicopter. Next we see a nuclear bomb set off at sea. They are trying to kill Godzilla.
1980s/90s Japan, some miners are digging and find a giant skeleton and what appears to be two giant eggs or cocoons. One has already hatched. Bryan Cranston is in Japan on the phone with someone at a nuclear power plant. He thinks something is wrong and wants the plant shutdown potentially. Turns out him and his wife both work there. Also his son tries to surprise him since it's Cranston's bday, but he doesn't notice. They go to the plant. The wife goes down below to the reactor maybe while Cranston talks to the people in the control room about shutting down the plant. Something goes wrong and the place blows up and Cranton's wife dies. We see their son looking at the crumbling plant from his school's window in awe.
Present day San Francisco, the son gets home from overseas duty (he's in the army, defuses bombs). He's an adult now with a family. He gets a call that his dad has been arrested in Japan. He goes there and picks him up from prison. Turns out Cranston thinks that the plant didn't meltdown, but it was something else. Cranston and his son go back to where the meltdown was to get some files from their old house. They get them and it turns out there is no radiation and that's weird. They get arrested again, but brought to the old plant site where it seems something is going on. There's a giant cocoon there they are studying and a similar thing starts happening at the plant meltdown. The cocoon hatches while Cranston is getting interrogated. All hell breaks loose as a giant monster starts destroying everything and Cranston gets mortally injured and dies.
The son is now being questioned by this Japanese scientist. Turns out these monsters thrive on radiation. Hence no radiation and why the plant got destroyed initially. They ask if Cranston had any leads, he tells them about echolocation which I guess the monsters use to find each other or radiation or something? Anyway, there are two monsters: 1 winged (male) and 1 wingless that just hatched (female). I guess they need radiation to lay eggs. At some point the Japanese scientist reveals the pocket watch and that his grandfather was in Hiroshima when they originally tried to kill Godzilla.
Godzilla shows up. The military think he's a bad guy and follow him. The scientist thinks he's the ultimate apex predator going after these weird monsters. The military has this plan to draw the monsters with a multi-megaton warhead off the coast of San Fran (for some reason). So all the monsters go there and we see the winged monster steal the warhead and give it to female monster (they kind of kiss, it's weird). She lays her eggs in a hole in the ground. Godzilla shows up and starts fighting the monsters shortly after this. They are teaming up and sort of winning.
The son decides to help the military defuse the warhead after the monsters steal it because now it's in downtown San Fran. They find it in the monster nest, but can't defuse it so take it to a ship and plan to boat it as far out to sea as possible. There's an oil tanker in the monster's nest and they use it to blow up the eggs as they are leaving. The explosion draws the monsters away from the fight, giving Godzilla the opportunity to kill the winged one.
They all get to the boat with the warhead, but remaining female monster shows up and kills everyone but the son. He is about to get killed next but Godzilla shows up and kills that monster. He then boats off with the warhead and prepares to die from his injuries and the explosion, when a helicopter saves him and he is reunited with his family. We see Godzilla collapsed in San Fran and he appears dead from wounds he took in the fight. But he gets up and returns to the ocean and everyone cheers for him. The end.
