Dr. Emma Russell wakes up recalling the SF Godzilla rampage incident. Maddie, her daughter is in kitchen echatting with her estranged dad Mark Russell. Emma goes to a lab with daughter Maddie, they are in central China, at a Monarch Facility housing a giant moth larva. The moth stirs but Emma gets it to settle down by finding a correct frequency on her Orca device, a packing case sized electronic apparatus. Suddenly, explosions and gunfire, a squad of soldiers come in and take Maddie and Emma and the orca device.
Dr. Serizawa, Dr. Graham and Sam Coleman are being grilled by a US Govt Committee on what Monarch is doing. Serizawa says the research is important to coexist with the Titans. Suddenly he gets a call and has to leave, the Monarch trio depart.
Mark Russell is in the woods sound recording wolves in a feeding frenzy. The Monarch leadership trio arrive by V22 Osprey and go back to his cabin. They show video clips of Maddie and Emma being taken. He agrees to go with them.
After SF, the couple diverged, Emma doing research , Mark leaving it all behind, they had lost a son and separated leaving Maddie with mom. Mark had invented the orca device to communicate with killer whales, he was unaware Emma had been developing it for Titans.
On an ocean platform Bravo near Bermuda Monarch has a large control centre, they can track Godzilla as he travels in the oceans around the world. Suddenly the signals get stronger, Godzilla is approaching. Monarch readies weapons but Mark says to stand down,they power down weapons and open the blast shields. Godzilla swims close by seemingly staring at the humans inside, the titan then zooms off. Mark asks to see the tracks history and the they show Godzilla has been repeatedly going near the Monarch Antartica Base.
Colonel Jonah Alan, a disaffected British soldier and his team assault the Antarctica Base, they kill the Monarch guards and force their way down, a Titan, Zero is entombed in ice. The soldiers plant explosives in the ice and prepare to detonate, they get word a Monarch team is approaching.
The giant Monarch flying wing arrives and deploys several V22s, The aircraft land and soldiers get out and start a firefight with Col. Alan's mercenaries. Mark Russell follows at a distance. He makes it close to where the two groups have a standoff on a Gantry. Mark sees Maddie and urges her to come, she starts but Emma tells her to stay. Emma the presses the red button and detonates the explosives. The entire facility begins to collapse and the two sides scramble to escape. Col. Alan, Emma and Maddie make it to their V22 and lift off. Mark saves a group of soldiers and is a little later in getting to their aircraft.
Meanwhile Titan Zero, a huge three-headed dragon breaks out of the ice, it notices the remaining V22 and approaches, ready to spew flames but Emma calms it down with her Orca device from the hovering Osprey, then they fly off.
Suddenly Godzillla appears and fights the larger three-headed monster. The Monarch team on the ground scramble to avoid being trampled. The three-head manages to push Godzilla into a crevice and flies off. The Monarch team is recovered. Mark says they have to find Godzilla.
There are 17 Monarch sites at dormant Titan locations. The one in Mexico is showing some movement, the flying wing heads to Mexico. A giant black bird with flaming tail feathers climbs out of a volcano, Rodan. Mark urges Monarch to evacuate the 11,000 people living close to the Mountain. Monarch notices a large hurricane also moving to Mexico, it is Titan Zero which can somehow control the weather.
V22 Ospreys rescue people and fight Rodan, the flying wing tries to draw Rodan toward Titan Zero. Rodan knocks down the V22 one by one. Again Godzilla appears and starts fighting Titan Zero in the Gulf of Mexico. Admiral Stenz comes on and tells the Monarch flying wing to get clear, the military has launched an oxygen-depleting cruise missile at Titan Zero.
One last Osprey calls a mayday, it is full of kids. Mark goes to the Landing Bay and ejects a parked Osprey making room for the craft, which manages a hard but safe landing inside the flying wing. The wing zooms off as the bomb explodes, a large shockwave expands and the area is quietened. After a moment Titan Zero gets out of sea, missing a head and flies to the top of the volcano, screeching into the air. The head re-grows. The Monarch team lose Godzilla's signal and think it has died.
Back on Bravo, Monarch determines Titan Zero is King Ghidra, the competition to Godzilla as the top apex predator on earth. All the other dormant Titans around to world start to awake and wreak havoc. Monarch scientist Ilene Chen explains Ghidra is an extra-terrestrial with greater powers than the others.
Mom makes a video call to Monarch to explain what she did. She thinks humans are over populating and destroying earth, releasing the Titans will restore the balance and save the planet. Mark and Monarch think she is crazy and has acted beyond her authority. Emma urges them to find bunkers to hideout until it's safe enough. Monarch decides to go look for Godzilla.
In China the larva transforms to a large moth, the older Dr. Chen basking in the beauty of the friendly giant.
Serizawa and Russell take a submarine and find a submerged city older than Egyptian ruins. Radiation keeps them back but a probe manages to get a photo of a sleeping Godzilla in a dry chamber. Serizawa volunteers to take a nuclear bomb to GodZilla to give him a healthy shot of energy. He takes a one man craft to the chamber, climbs up beside Godzilla, pats it's nose and says goodbye. The bomb explodes.
The submarine surfaces and they lookout for signs on the surface. A large whirlpool starts and Godzilla comes out, the Titan comes close to the sub, peers closely, but leaves them alone then swims off. Back at Bravo, Mark wants to find Maddie and prepares to leave, but a bright light breaks through the rain, it is Mothra in all its glory.
Maddie has also realized her mother is crazy and tries to stop her. Emma realizes they can use Boston's Fenway Park to send out a Orca signal stopping the Titans, Col. Alan says no, they must see through the plan, even though Ghidra's powers were more than expected.
Maddie escapes the Monarch bunker, an old fallout shelter, with the orca device. She makes her way to Fenway Park and plugs the equipment into the PA system, then starts broadcasting a signal.
The Titans around the world stop, Ghidra goes toward Boston to find the signal. It arrives in a hurricane and blasts the PA speakers, then looks into the stadium windows seeing Maddie. Maddie grabs the orca and tries to run for it. On the baseball field she loses the case and Ghidra is about to blast her when suddenly a blue blast knocks the three headed-monster down. Maddie looks and sees an angry Godzilla walking ashore with a supporting squadron of V22 firing rockets and the flying wing.
Godzilla and Ghidra now fight again in Boston, Mothra and Rodan fight in the air. Once again Ghidra seems to get the better of Godzilla who is left panting in the rubble. Mothra kills Rodan then attacks Ghidra, who destroys Mothra with a blast. The Mothra particles float down onto Godzilla.
The Monarch team go to find Maddie, they find the orca but not the girl. Meanwhile, Emma has had a change of heart and also arrives at Fenway Park, she saves the Monarch team and they escape in a Hummer, followed by Ghidra. They try to give Godzilla time to recover. The parents realize Maddie went to their old family home and go there, finding her in the ruins of the house. Maddie recovers and they plan to use the orca device again. A V22 arrives to take the team away, everyone but Emma get onboard, she stays on the ground and says sorry, she activates the orca and Ghidra blasts her position. Mark and Maddie look on in grief.
Godzilla recovers, now glowing red he fights again this time finally destroying Ghidra. Other Titans arrive in Boston and kneel before Godzilla. He stands high and mighty, the King of Monsters.