Chau and his associates have fled to their bunker as Otachi storms the city. Dr. Geiszler has been pushed out into the streets, and heads to a public Kaiju bunker.
However, when it sounds like the creature has settled directly over them, he begins to panic that Chau may have been right, and that it may be looking for him.
As if to answer that, bunker is attacked by Otachi. The ceiling caves in, and the Kaiju attempts to reach him.
Just then Gypsy Danger appears and attacks Otachi. The battle goes through many buildings and they fight through the city streets.
Then the battle takes a turn when the creature suddenly sprouts wings and begins to carry the Jaeger in her clutches into Earth's upper atmosphere.
Activating the Jaeger's chain-sword, they manage to destroy it before plummeting back to Earth, barely regaining control of the Jaeger as a team to make a safe landing.
Raleigh and Mako return to the Shatterdome to cheers as the pilots of the Striker Eureka also voice their thanks and appreciation.
During the jubilation, Raleigh notes Pentecost bleeding slightly from both nostrils.
Meanwhile, Geiszler has returned to Chau's store and demands claim over the dead Kaiju's brain. Chau relents, and he and his team go to harvest the parts from the carcass.
Chau's men say that the second brain of the Otachi is damaged, but they hear a heartbeat, and Newton realizes that Otachi was pregnant.
Just then, an infant Kaiju breaks through a slit in the side of its Mother, and attempts to escape before falling down, seemingly choking on it's own umbilical cord.
As Chau gloats over the dead infant Kaiju, claiming he knew it couldn't survive very long outside it's mother, the creature rears up and swallows him whole. The infant creature finally dies in the street.
At the Shatterdome and in private, Pentecost explains to Raleigh how in the earlier days of the Jaeger program, shielding from nuclear contaminants had not been considered. Due to radiation poisoning from piloting the Mark-1 Coyote Tango, his condition has been worsening over time.
Dr. Gottlieb soon shows up in Hong Kong with Geiszler's machine, and though the first attempt almost killed him, Gottlieb volunteers to drift with Geiszler, to cooperate in learning more through the infant Kaiju's brain.
Stacker decides to put the final plan into motion early, knowing that they won't survive the triple attack Gottlieb predicted. The final plan is to go through the portal and destroy it with a high-yield nuclear bomb, so that the Kaiju can no longer get through. The Gipsy Danger is supposed to run protection, giving enough time for Striker Eureka to get to the portal to deploy the bomb.
However, with Herc injured, and little time to find another pilot, Pentecost surprises everyone when he decides to partner with Chuck, knowing that they could all die if he didn't. The strain of piloting a Jaeger could prove fatal to Pentecost, but he volunteers anyway.
Herc and Chuck say goodbye to each other, knowing that Chuck will most likely not return. As the two Jaegers near the rift, Geiszler and Gottlieb rush into the Shatterdome's control room, and explain that the plan will not work.
The channel between dimensions will only respond to the genetic code of a Kaiju, the very reason for the previous failures to destroy the channel with other nuclear weapons. If they attempt to drop the warhead into the channel, it'll just deflect out. They must use a Kaiju or a part of one to get through the portal to destroy it.
The two Jaegers engage the Triple Event Kaiju guarding the rift - Scunner, Raiju and Slattern - with the latter the strongest of the three, the first Category V Kaiju.
Gypsy Danger and Striker Eureka sustain heavy damage in the battle.
Stacker and Chuck decide to deploy the bomb, sacrificing Striker and themselves to try and kill Scunner and Slattern to give Mako and Raleigh a chance to get through the portal.
A heavily damaged Gipsy approaches the portal but is attacked by a weakened, though not dead Slattern. Gipsy tackles Slattern, killing it with her sword and chest turbine, then passes through the portal latched onto its corpse, bypassing the code that would reject any non-kaiju.
Inside the Kaiju world, the Gipsy Danger crew are losing oxygen rapidly, so Raleigh gives Mako his share, and deploys her ejection pod. He then manually initiates the detonation of the nuclear core.
As Gypsy Danger enters the Anteverse, Raleigh ejects himself out and back to Earth seconds before the mech detonates, decimating the alien forces and sealing off the Breach.
The two pods reach the surface, but Raleigh's is not responding with a pulse, and they fear that he is dead.
Mako swims to Raleigh's pod, opening it, and hugging him in relief. He jokes that he couldn't breathe because she was holding him too tightly. Tendo tells them that helicopters are on their way to get them, and that they've done well. Herc then addresses the Shatterdome as "Marshal," telling them to stop the war clock that counted down how much more time until the next attack, and the PPDC breaks out in cheers.
A mid-credits scene reveals that Hannibal Chau survived being swallowed by the baby Kaiju by cutting his way out with a pocket knife. He angrily asks where is his lost shoe.
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