The crypto-zoological agency Monarch faces off against a battery of god-sized monsters, including the mighty Godzilla, who collides with Mothra, Rodan, and his ultimate nemesis, the three-headed King Ghidorah.
Several years after Godzilla’s emergence in San Francisco, Dr. Emma Russell and her daughter Madison are taken by eco-terrorist Alan Jonah and his team to awaken King Ghidorah using a device Emma created called The Orca, which emits frequencies used to communicate with Titans. Jonah witnesses the Orca’s capablities when Emma uses it to tame a newly-hatched Mothra.
Emma’s ex-husband Mark has joined Monarch’s team of scientists and soldiers to prevent Jonah from getting what he wants, but they are too late to stop Emma as she frees Ghidorah. The beast goes on a rampage and takes down Godzilla in their initial fight. Emma reveals to Mark that she has been working with Jonah to unleash the Titans upon the Earth to bring balance back to it. After freeing Rodan from his volcano, he kills a whole squadron of soldiers before fighting and losing to Ghidorah. The three-headed dragon then establishes his dominance, leading the other Titans to rise and wreak havoc.
The military fires a bomb that severely weakens Godzilla. He is recuperating underground, but Monarch knows that a nuke would speed up the healing process. Dr. Serizawa voluntarily goes down there to sacrifice himself to help Godzilla back up.
After seeing the harm she’s caused, Emma breaks ties with Jonah and goes into Boston to get Madison after she takes the Orca to Fenway Park to call the Titans there. This leads to an epic battle between Godzilla and Mothra against Ghidorah and Rodan. Mothra beats Rodan, but as Ghidorah weakens Godzilla, she makes a sacrifice to get vaporized by Ghidorah, but allowing her essence to empower Godzilla. Emma stays behind to lure Ghidorah away from Godzilla with the Orca, losing her life in the process. Godzilla then emits a nuclear pulse from the nuke that gives him enough power to completely fry Ghidorah. The other Titans then come and bow before Godzilla, their new leader.
The credits indicate that a Mothra egg has been found, while things are being set up for Godzilla to battle Kong. Meanwhile, Jonah is given one of Ghidorah’s head to use for an experiment.
The film starts in San Francisco in 2014. Following the deadly battle that took place there, Mark (Kyle Chandler) and Emma Russell (Vera Farmiga) have lost their eldest son Andrew, while holding onto their young daughter Madison (Lexi Rabe). Emma looks up and catches a glimpse of Godzilla himself, somewhere after his battle with the MUTOS.
In the present, Mark and Emma are separated, and she works as a paleobiologist for Monarch while living with Madison (now played by Millie Bobby Brown). She has been working on a device called The Orca, which can create frequencies used for communicating with Titans. Mark still tries to maintain contact with them for Madison’s sake. Emma and Madison later go to an underground facility in China where other scientists are witnessing the birth of Mothra. As she emerges, she spots soldiers with weapons drawn on her, and she reacts violently, shooting them with webbing. Emma runs to try and activate the Orca and manages to find a frequency that Mothra can understand, which calms her down. Madison is even able to approach her and touch her. Unfortunately, the moment is ruined when a group of eco-terrorists led by Alan Jonah (Charles Dance) come in, kill the remaining scientists, and kidnap Emma and Madison. Mothra manages to escape.
At a Monarch senate hearing, Dr. Ishiro Serizawa (Ken Watanabe), Dr. Vivienne Graham (Sally Hawkins), and Dr. Sam Coleman (Thomas Middleditch) walk out after the senators demand that Monarch be integrated into the U.S. government. They later meet with Mark after learning that Emma and Madison were taken by Jonah, as he wants to use the Orca for his own nefarious purposes. The three take Mark with them to meet other Monarch employees, such as sonographer Dr. Rick Stanton (Bradley Whitford) and mythologist Dr. Ilene Chen (Ziyi Zhang), as well as G-Team leader Colonel Diane Foster (Aisha Hinds) and Officer Jackson Barnes (O’Shea Jackson, Jr.). They inform Mark that many other Titans besides Godzilla have been discovered, and although he suggests killing them before they come out (he seems to blame Godzilla for Andrew’s death), Monarch refuses to let that happen. They then show him that they have Godzilla contained, but they are now setting him free so that he may trust them. Godzilla then swims toward Antarctica, and Monarch follows.
Jonah brings Emma and Madison to a site where a colossal creature dubbed “Monster Zero” – King Ghidorah – lays encased in solid ice. They set up the Orca to try and communicate with him, when Monarch and Jonah’s team eventually clash. Mark tries to rescue Emma and Madison, but as Madison starts walking toward him, Emma grabs a detonator, intending to set off the explosives all around the ice to free Ghidorah. She does so, and everyone runs for it. The three-headed beast is freed and he rises to the surface. Not long after, Godzilla comes in to fight. The two monsters engage in a smackdown, with Godzilla trying to fire his atomic breath at Ghidorah, but he dodges and fires lightning from all three heads, plunging Godzilla back into the ice. Ghidorah then proceeds to rampage, killing a number of people, including Graham.
In the aftermath, Monarch makes contact with Emma, who is willingly working with Jonah to free the Titans. In their eyes, the Titans are the planet’s rightful rulers, and they may bring a balance back to the world that man has long since ruined. Mark thinks she is doing this in retribution for Andrew’s death.
Jonah and Emma head with their team toward Mexico to free another Titan. The city starts to get evacuated. They make their way to an active volcano to unleash Rodan, “the Fire Demon”. He emerges as Monarch’s squadron of fighter pilots head in to try and take him down. They prove to be no match for the winged beast, as he devours some of the pilots while finishing the rest of them by barrel-rolling through the air. Not long after, Ghidorah comes in and battles Rodan. Ghidorah gains the upper hand (or claw) by using his extra heads to take Rodan down. Before he can continue to attack, Godzilla comes back for round two. They start to duke it out again, with Godzilla managing to tear off Rodan’s left head. Meanwhile, Monarch is contacted by Captain William Stenz (David Straithairn), who tells them that the military is about to launch a massive bomb called the “Oxygen Destroyer” in order to kill the beasts. The bomb hits, but Ghidorah escapes, while it looks as though Godzilla has perished.
Ghidorah flies to the top of the volcano where he regenerates his head. He emits his call, which awakens the rest of the sleeping Titans. In response, the Titans begin to cause untold mayhem and destruction upon their lands, with countless lives being lost. Rodan even submits to Ghidorah’s rule, because, as Monarch notes, Ghidorah has established himself as the alpha among the Titans, so they all follow him now.
Mothra, who has been in a cocoon behind a waterfall, emerges with glorious glowing wings, and she flies her way toward Godzilla, who is alive but weakened, and is recuperating underwater. Monarch locates the two, as Mothra is communicating with Godzilla. The team determines that Mothra is like the queen of the monsters, so she and Godzilla “have a thing”, as Barnes notes. Ilene also points out through old text that Ghidorah was among the most feared of the Titans, and he would challenge Godzilla for supremacy.
Mark heads with Serizawa, Ilene, and Coleman toward Godzilla’s location in an attempt to revive him, but it is noted that it could take years for his healing process to fully get him back on his feet. The scientists realize that since Titans like Godzilla feed on radiation, they can detonate a nuke that will heal him faster. However, the sub’s weapons systems is offline after sustaining serious damage, so Serizawa makes the choice to take the nuke down there himself and set it off. He bids farewell to his colleagues and makes his way up to Godzilla, the closest he has ever gotten to him. He pets a barely conscious Godzilla before telling him goodbye and detonating the nuke, sacrificing himself. Soon, Big G emerges more powerful than before, and he fires his atomic breath into the sky.
By now, Emma has realized that her original plan has gone out of control, and that Ghidorah is leading the Titans to cause more destruction. Even Madison has chewed her mom out for it, calling her a monster. Emma tells Jonah that since Fenway Park and most of Boston has been evacuated, they can use the Orca to broadcast a frequency through there, but Jonah turns his back on Emma. Madison steals the Orca and heads to Fenway Park herself, sending out the frequency that is strong enough to attract the Titans to that location. Ghidorah arrives, as does Godzilla, and they continue to rampage in their final showdown across the city while Madison heads for cover.
Mark informs the Monarch team that Emma created the Orca with mixed frequencies from Godzilla and humans, so humanity has as much of a part in this battle as the Titans do. They also see that Godzilla is emitting a massive nuclear pulse, and he is set to go off soon. Mark heads into the city to find Madison, and they eventually come across Emma, who has fled from Jonah to save her daughter. They determine that Madison has gone to their old home, and sure enough they find her there under the rubble, unconscious but alive.
Godzilla and Ghidorah go at it again, with the three heads chomping into Godzilla’s sides. Up in the sky, a beam of light emerges, and Mothra swoops down to help Godzilla out by webbing the three heads. Rodan returns and attacks Mothra, nearly taking her head off until she outsmarts him and takes him down by jabbing her stinger into his shoulder. Ghidorah has now weakened Godzilla, and Mothra goes by her friend’s side. She rises toward Ghidorah, but the beast fires his lightning and vaporizes her, and her essence covers Godzilla to invigorate him. In a rage, Godzilla rises to continue attacking his nemesis. Meanwhile, the humans try to get the hell out of Boston, but Emma knows she must redeem herself for what she started. She declines to get on the aircraft out of the city, even as Mark and Madison plead with her to join them. She takes a van and uses the Orca to lure Ghidorah toward her. He fires a blast at her, which only knocks her out of the van, but has bought Godzilla enough time to get his nuclear pulse building. Before dying, Emma looks up and declares, “Long live the king.” Skyscrapers melt around him while everything else bursts into flames. Finally, Big G delivers a powerful blast toward Ghidorah, first to singe off his wings and then to take out his two side heads. After one more blast, the city becomes toast, and from the smoke, it appears that Ghidorah’s head is emerging…except it’s inside Godzilla’s mouth, and he finishes off the beast once and for all.
Soon, the other Titans arrive in what remains of Boston. They all bow before Godzilla, even Rodan. Mark, Madison, and the rest of Monarch watch in astonishment. Godzilla then lets out a triumphant roar.
During the credits, we see newspaper articles making notes that a Mothra egg has been discovered (meaning she can come back), while continuing to document ongoing activity in Skull Island. We see more cave drawings, including one in which Godzilla battles the world’s other most well-known Titan…KONG.
After the credits, in Isla De Mara, Jonah and his men follow a man who presents them with one of Ghidorah’s heads. Jonah says he will take it, intending to use it for an as-yet-unknown purpose.