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Pacific Rim Uprising made some pretty significant changes to the status quo of the first film, some of which haven't sat well with many fans. Now, director Steven S. DeKnight has explained why the film made its single, most significant, decision. That decision, and this is a spoiler if you haven't seen Uprising, is that the movie kills off the character of Mako Mori, the most popular character in the original movie. Steven S. DeKnight takes full responsibility for the decision, though he doesn't take it lightly. He says that the decision to kill off the character was made because the story required it, so much so that the sequence was in the movie even before the character was. According to DeKnight...
To me, at the end of the day, all other concerns must be set aside in service of the story. For example, at one point Mako wasn't even in the movie. Instead Herc was the one in the helicopter, playing the Mako role. And his fate was exactly the same.
Steven S. DeKnight takes a pretty deep dive into a lot that we didn't know about Pacific Rim Uprising on Twitter as a response to a fan who expressed his disappointment with the way Mako Mori's character was handled in the sequel. It turns out that, while Mori's fate was always going to be what it was, with her being the victim of a helicopter crash caused by a rogue Jaeger, there was originally going to be a lot more done with the death.
Originally, there were more scenes with Mako Mori in them earlier in the movie and more scenes afterward which dealt with the death, giving the big moment more weight in the film. Unfortunately, these other scenes were either cut, including a sequence where Mako explains to her brother Jake (John Boyega) what happened to Raleigh Beckett, the co-lead of the first film, and why she can't pilot a Jaeger anymore, or they were never filmed, like a massive funeral for Mori that included a Jaeger honor guard.
Interestingly, Steve S. DeKnight also reveals that in the original treatment of the movie, Mori actually survives the crash, but is still out of action for the duration.
The most painful thing that never made it before the camera was something from the original outline. In that, Mako survived the initial crash but was in a coma...Raleigh (he was still the lead at the time) drifts with her to go into her mind to pull her out of the coma. It was during this sequence that he saw the "Kaiju head" clue...This was regrettably cut because of the sentiment that coma was too depressing.
In the end, DeKnight says that Uprising was always meant to be the second part of a trilogy, and that "a concept revolving around Mako" was meant to be a big part of the third movie. The director won't elaborate on this, and one has to wonder if the reason why is because some element of this idea could still be part of a third Pacific Rim movie. Uprising clearly set up a third film, and with overseas box office numbers, the movie did quite well, so there's a decent chance we could see that third film come to life.