BEWARE OF SPOILERS!
Plot5 years have passed since the 2014 San Francisco incident where Godzilla battled the MUTOs and won, but still several human casualties occurred and many mourn their deceased loved ones while the world still lives in fear that monsters will again ravage civilization. Capital cities across the globe are flooded by crowds angrily rallying for immediate extermination of these gigantic creatures (Titans). The Russell family is grieving the loss of their youngest son Andrew who died during the 2014 incident. The patriarch Mark Russell is a wildlife photographer who spends time away from his family and is currently documenting wolves. His daughter is Madison and his wife is Emma, a paleobiologist affiliated with MONARCH, the organization that researches information about the monsters while also keeping them contained.
Madison and Emma are currently stationed at a Monarch outpost in China witnessing the birth of larva Mothra, who after going berserk is calmed down with the man-made sound wave system ORCA when a supervisor at first tries to kill Mothra with the emergency shut-down button. Suddenly, the MONARCH guards monitoring Mothra are shot down by gunmen, whose leader orders Emma and Madison subdued as while Mothra escapes and undergoes cocooning in a waterfall.
Monarchs Dr. Serizawa, Coleman and Vivianne Graham are all trying to convince the Senate not to give in to the masses pleas to destroy all monsters. Serizawa claims Godzilla is an essential and vital key player in the Earths ecosystem, then walks out the Senate hearing as no deal could be reached. Monarch then reveals to Mark Russell that his wife and daughter have been kidnapped by Alan Jonah, a British eco-terrorist who is after the ORCA. Mark Russell helped develop the ORCA as a means of interpreting whale songs, but Jonah now has plans to use the ORCA to unleash the monsters upon the earth. Mark fears that the monsters are too dangerous to be kept alive by Monarch and believes Godzilla is a threat to humanity, ordering Godzilla be terminated against Serizawas wishes. Mark enters a high-tech ship Monarch designed to follow the monsters and they enter the seas to find Godzilla, who has been missing for 5 years. To prove to Godzilla they are not a threat, Mark orders Monarch to lower their shields and show themselves to Godzilla (without reacting at all). Godzilla does not attack them, but he does move past their ship rocking it. Mark and Monarch in their ship follow Godzilla to see where hes going.
Jonah takes Emma and Madison to Antarctica where a monster (Monster Zero) frozen in ice is also being guarded by Monarch. Jonahs men shoot down the Antarctic outpost guards while Monarch and Mark arrive in Chinooks to intervene. Mark using a gun orders Jonah to release his wife and children, but suddenly Emma grabs the detonator that frees Ghidorah. While retreating back to their ship, Ghidorah destroys their Chinooks and kills off their soldiers who try firing at him. Emma tries hindering Ghidorahs rampage with the ORCA but it is only delaying his attacks, not completely suppressing him. Ghidorah then pauses when he senses the presence of his arch nemesis Godzilla (whom he battled since prehistoric times), and Godzilla engages in battle with him thus allowing the humans to make a run for it. Unfortunately for the humans, Godzilla is not strong or powerful enough to take down Ghidorah on a frozen tundra and Ghidorah ends up eating Graham. The United States Air Force arrives firing a barrage of missiles at Ghidorah. Deciding hes outnumbered against Godzilla and the human armies, Ghidorah retreats.
Emma sends a video signal to Monarch rationalizing her decision to free Ghidorah, claiming that the Titans (the codename for Kaiju) are helping restore the Earth back to its green, natural state after humans depleted its natural resources through overpopulation, pollution, mining and burning fossil fuels. Mark argues that Emma risked putting their own daughters life at stake by freeing Ghidorah, and Monarch brands Emma a traitor to humanity for freeing a tyrant monster who has no benevolent intentions for humans OR monsters whatsoever. Monarch deduces that Ghidorah will terraform the earth to its own liking when their expert Dr. Illene Chan reveals that Ghidorah is from space, and so he is not of Earth, hes an invading alien. Meanwhile, the presence of Ghidorah is rocking the earth as many monsters are waking up due to sensing Ghidorah and they are ravaging and devastating human cities to clear the earth for Ghidorahs own terraforming purposes. This means of course that all because of Emma, Ghidorah has enslaved the Earths monster population and is forcing them to wipe out humanity into extinction.
Monarch hatches an idea to make Rodan, the red Pterodactyl-like monster who has been living dormant inside a volcano in Mexico, to fend off Ghidorah. As Rodan emerges, Monarch baits him into Ghidorah with the hopes that he can kill Ghidorah. Instead, Ghidorah easily defeats Rodan in battle. The United States Army declares that they will use their new top super weapon called the Oxygen Destroyer against Ghidorah. Ghidorah gives chase to the Monarch ship but Godzilla intervenes, battling him in the seas where Godzilla has a tactical home field advantage being able to cut off one of Ghidorahs heads. However, the Oxygen Destroyer strikes Godzilla and his heart stops beating while Ghidorah is unaffected and flies off. Dr. Serizawa is devastated fearing that Godzilla is now dead, and condemns Mark for ever wanting Godzilla dead. Ghidorah then forces Rodan to bow to him, forcing Rodan to become yet another slave of his. Emma starts regretting freeing Ghidorah when she finds that Ghidorah isnt exactly restoring balance to Earths ecosystem so much as only exacerbating destruction, and Madison claims her mother is a monster. Emma argues with Alan if their plan to have released Ghidorah was such a wise one.
Monarch concludes that Godzilla has retreated to an underwater volcanic valley that was once a civilized kingdom but has sunken below water to recuperate from the Oxygen Destroyer, and Mark claims that in order to save Godzilla they must fire a nuclear warhead at him so he can regain his energy back. With their warhead firing systems damaged in the battle, Serizawa volunteers to start the warhead himself at the cost of his own life. Using a miniature submarine, Serizawa hurries to the man-made temple Godzilla is resting upon and activates the warhead, where he tells Godzilla, Goodbye old friend. The warhead detonates, Godzilla is revived. Mark then orders the rest of his team not to be frightened and act calm when Godzilla looks at them in-person. Marks strategy works, and Godzilla rushes off to go fight Ghidorah.
Suddenly, all the monsters tearing apart cities under Ghidorahs influence have stopped rampaging. We then see that Madison stole the ORCA herself, mixed human voices into the ORCA sound signal to lure the monsters in to Fenway Park. Madison also escapes Jonahs captivity by sneaking through the ducts (so that not even her mother can hear her). Ghidorah flies to Washington D.C. where he and Rodan are battling the humans. Upon discovering Madison is missing, Madison forces Jonah at gunpoint to let her take a car and look for her daughter. Jonah without hesitation allows her. Mark also arrives at Fenway looking for Madison. Mark and Emma reunite arguing and blaming one another for Madisons disappearance. Ghidorah, who is looking to destroy the ORCA so that he can maintain his dominance over the rest of the monsters, hunts down Madison and starts firing his lightning rays at her. Madison is saved just in time by Godzilla. The United States military lends air support to Godzilla in combating Ghidorah. Dr. Rick Stanton however warns that the warhead Godzilla has absorbed is making his temperature elevate and he will soon undergo a thermonuclear phase that will make him enter a burning stage.
Godzilla struggles in his fight against Ghidorah. A newly hatched Mothra arrives and lends her support to Godzilla, but her assistance is very short-lived as Rodan attacks Mothra. Mothra pierces Rodan with one of her stingers so that hell be unable to continue fighting, and as Ghidorah battle injures Godzilla preparing to kill him, Mothra kamikazes herself at Ghidorah only to be blasted away and she starts decaying, but transfers her remaining energy to Godzilla. Ghidorah then does what was believed to be impossible: picking up Godzilla. He snatches Godzilla, brings him high to the sky, and drops him in to the ground. Emma then sacrifices herself to help Godzilla win the battle by using the ORCA to distract Ghidorah in her car. Ghidorah kills Emma in the process by blasting away lightning at her car, shocking her to death but with her dying breath she blesses Godzilla to win and says, "Long live the king". As Mark and Madison mourn for Emmas death, a newly healed Godzilla enters the thermonuclear phase as Stanton predicted and he uses nuclear pulses to finally finish off Ghidorah, killing off two of its heads then finally ripping off one of the heads, putting it in his mouth and releasing his atomic breath once more, completely atomizing the remaining Ghidorahs head.
Godzilla then turns around to see himself approached by Behemoth, Scylla, a female MUTO and Methuselah. They were all lured into Fenway Park by the ORCA signal Madison sent out. Rodan snarls at Godzilla apparently challenging him to a fight, but one angry glare from Godzilla convinces Rodan to instead bow to him, and the rest of the Kaiju bow as well. Godzilla roars in triumph having reclaimed his rightful place as the King of the Monsters.
The ending credits reveal that the Kaiju under Godzillas leadership are helping bring balance to the ecosystem and environment by helping endangered species such as fish recover, reversing global warming stopping the polar ice caps from melting, helping rainforests grow back to fruition and even provide excellent fertilizer. Monarch gladly relinquishes all classified information and research on the monsters to the public as while continuing to study the Kaiju and their origins further. A second Mothra egg has been spotted, Godzilla orders all Titans to keep clear of human territory, and one cave drawing depicts Godzilla fighting Kong.
In a post-credits scene, Alan Jonah finds a head of Ghidorah and purchases it from a fisherman with plans for regenerating Ghidorah anticipating he can one day expunge humanity and Godzilla.