Eventually, another pilot is chosen for Raleigh, but against his better judgement, Stacker appoints Mako as Raleigh's partner, and they do a test run in Gipsy Danger.
A test-run of Gypsy Danger within the Shatterdome appears to be going well. But after the link between Raleigh and Mako is established, Raleigh has a memory of his brother being taken from Gipsy Danger, causing the link to break.
Since it is Mako's first run, she gets lost in her memories. Inside the control room, Stacker is called away by a frightened Gottlieb, who tells him that Newton attempted the link anyway, and has collapsed in seizures on the floor.
Stacker runs to check on him. Geiszler theorizes that based on some Kaiju samples, what they were seeing coming through were cloned creatures, and his drift vision appears to corroborate his theory. Newton tells Pentecost that the Kaiju are a hive-mind, meaning that they were all mentally linked and that their masters are colonizers. He explains that they go from world to world, utilizing the Kaiju to eradicate the current inhabitants.
They came to Earth once before during the time of the Dinosaurs, but there was too much oxygen in the atmosphere and that the humans practically terraformed it for them. Stacker instructs Newton to do another link. Unfortunately, the Kaiju brain has been damaged, and Geiszler needs a fresher brain in order to learn more. Pentecost gives him a small card, and tells him he can get a fresh brain from a black market dealer. Pentecost instructs Newton to go to Hong Kong to look for a man named Hannibal Chau.
Back at the Gipsy Dancer, we continue with Mako's tragic memory. When Mako was a child, she lost her family to a Kaiju attack in Tokyo, Japan.
She wanders around Tokyo with the Kaiju, Onibaba, following her. Through their mind connection, Raleigh virtually witnesses her tragic memory.
When he notices she is looking up to the sky, he looks up also and sees a Jaeger suspended in air by helicopters.
Lost in her memory, Mako accidentally activates the plasma cannon, causing Herc and Tendo Choi, an engineer, to shut Gipsy Danger down.
Stacker returns, deciding that it is far too dangerous for the two of them to work together, and talks with Herc and Chuck to determine the next steps. Following the incident, Raleigh now understands more about Mako's past.
Meanwhile, Geiszler heads to Hong Kong where he finds Chau's place of business, and is greeted by Chau's Aide, the "Wizened Man."
Geiszler is impressed with Chau's secret room containing equipment and live specimens that even the government doesn't have, which could be useful in his theory.
Chau enters the room. He is actually an American going under an alias and a dealer in Kaiju remains. Chau collects them from battle sites and deals them on the black market.
Geiszler bats around Chau's arrogance and questioning demeanor, until he mentions how he drifted with a Kaiju brain.
This leads Chau to question that if he connected to the other side, what's to say those on the other side don't know what he now knows? Newton tells Chau that he wants to establish another link, but Chau tells him that it's dangerous because now the Kaiju know where Newton is and will want to kill him.
Back at the Shatterdome, Chuck and Raleigh fight when Chuck insults Mako, but are broken up by Herc, while Raleigh and Mako go in to talk to Stacker. Even with Mako becoming unfocused in the drift, Raleigh still wants her as his partner. But Stacker tells Mako that she is too inexperienced, she won't be piloting again, and Mako leaves. Raleigh strikes out at Stacker, saying that he knows why he won't let Mako fight, since he's been in her memories.
We are given the final piece to Mako's tragic memory of the attack on Tokyo. Just when it seemed the creature was going to kill her, a Jaeger was deployed that stopped it.
The pilot of the Jaeger was Pentecost, who is revealed to be able to pilot a Jaeger by himself, and he took her under his wing after that. Raleigh says that he is only hindering Mako, but Stacker says that he has made up his mind.
Shortly after their discussion, Tendo detects two Category IV Kaiju, Leatherback and Otachi, surfacing near Hong Kong.
On Pentecost's orders, Striker Eureka, Crimson Typhoon and Cherno Alpha are deployed to fend off the Kaiju. Herc and Chuck are supposed to remain back by the island as a last resort to avoid being damaged and protect the City's coastline.
Just as discussion had seemed to point to the Kaiju becoming more dangerous, the two that have emerged come with additional armaments.
Crimson Typhoon's crew, the Wei Tang triplets, take their Jaeger into the fight, but they are soon overwhelmed. Leatherback and Otachi swiftly destroy Crimson Typhoon.
Determined to "get those bastards," the Cherno Alpha attacks, but Otachi is endowed with the ability to shoot acid, which melts away Cherno Alpha's armor and they are eventually destroyed.
The father / son team piloting Striker Eureka abandon their orders to protect Hong Kong, and go at the creatures.
However, Leatherback lets loose an EMP burst that disables Striker Eureka, and the command center in the Shatterdome. Tendo says it will take two hours to get it all back online.
Striker Eureka is dead in the water. Raleigh gives a solution: though the newer models of Jaeger are digital, the Gypsy Danger is analog and it's nuclear core was unaffected by the EMP, thus more resistant to EMP attacks.
Pentecost sends out Raleigh and Mako, who end up destroying the EMP-bursting Kaiju after a protracted battle, saving the Hansens as well as Striker Eureka, though Herc breaks his arm after Leatherback lands a blow on the mech's head. However, Otachi ends up heading into Hong Kong.
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