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It's not a stretch to say that 13 Sentinels: Aegis Rim has one of the deepest stories of any game... probably ever. The game's plot covers pretty much every sci-fi concept under the sun, from alien invasions to time travel to mech battling and more.
Moreover, the game's story is told in a nonlinear fashion, where you can choose how to advance through the story and which of its 13 main characters to follow. The fact that the game's plot hangs together at all is a miracle, but given how complex the narrative ultimately becomes, it's not surprising that there are still a few loose ends when the credits finally roll.
Spoiler Warning
7 Is This Happening Elsewhere Too?
After you finish 13 Sentinels' main storyline, you might notice that the completion percentage on Analysis mode is less than 100 percent. If you enter this mode and scroll all the way to the end of the story, you'll find a hidden cutscene that shows the camera panning across the galaxy before landing on a scene that looks a lot like the game's opening... but features Minami and Ogata instead of Fuyusaka.
Does this mean that there are other clones out there fighting the same battles, and that the events of the game are playing out all across the galaxy? How many colonies managed to establish themselves?
6 How Did Sekigahara Get Here?
Sekigahara is one of the most interesting characters in the cast - when his story begins, he wakes up in an alley next to a dead body, with no idea of how he got there. He goes on the run from the police and spends most of the game evading capture while trying to piece together his lost memories.
But later, when we learn everyone in the game is a clone living in a simulation, we also discover that the original Sekigahara was a professional assassin. Everyone else was a scientist or a coder or had some kind of important skill; Sekigahara's skill is literally killing people, which seems like a strange fit for an attempt to restart humanity after the apocalypse. How did he get here?
5 Why Did Shinonome Think It Was A Good Idea To Destroy Humanity?
Ryoko Shinonome is one of the most mysterious characters in 13 Sentinels; she's stricken with amnesia and forced to take mysterious pills that either preserve her body or further destroy her memory. Eventually, we learn that there's even more darkness hidden in her story: after having her heart broken and witnessing all of her friends die, Shinonome's original incarnation decided to infect the simulation with the kaiju, causing the system to reset each time the clones were ready to restart humanity.
Essentially, she was dooming humanity to extinction. Surviving a mass extinction event is traumatic, sure, but how did she decide to essentially repeat that process?
4 How Does Miura Have A Scar When He's In His Sentinel?
It's revealed late in the game that when the characters are supposedly in the cockpit of their Sentinels, surrounded by machinery and viewing the simulation as a top-down wireframe rendering, they're actually seeing their clone pods and underlying coding of their everyday lives. This means that the battles are a more accurate depiction of reality than their day-to-day lives in 1985, 1945, 2025, or what have you.
So if the Sentinels are real and the virtual world isn't... how does Miura still have a scar when we see him in his Sentinel, given that he received the scar in the virtual rendering of 1945? Are injuries sustained in the simulation transferred onto the clones' real-life bodies?
3 What Happened To Okino And Tamao?
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While 13 Sentinels follows 13 clones of the humans who survived the nanomachine virus, there are two other characters who play major roles in the story, Tsukasa Okino and Tamao Kurabe. Both of them were also cloned, but died prior to the events of the current simulation.
In simulations where all of the clones die, the whole simulation resets and new clones are created; however, since only Okino and Tamao died, the game never quite answers what happened to them. Were their bodies destroyed, leaving only their AI presence in the simulation? Will they return in the future?
2 Why Are They Still Using Nanomachines?
13 Sentinels takes place in a future world where nanomachines have not only been invented but have been injected into nearly everyone. This means that when a mysterious virus targets nanomachines, the whole population is susceptible and there's no way to formulate a cure in time. This leads to near-total human extinction, and the only hope that remains is with a small group of clones... who are built and rebuilt using nanomachines... and have them implanted in their bodies.
I understand that the technology is ubiquitous, but wouldn't the clones be susceptible to the virus as well, leading to another extinction event?
1 Isn't This All A Little Complicated?
In order to combat the deadly nanomachine virus and save humanity, the remaining survivors formulated a simple plan. Step one: clone a small group of survivors. Step two: have them live in a virtual simulation of past eras, separated by 40 years each, which should somehow teach each of them some useful skills and thought processes. Step three: destroy the clones and restart the whole process if anything goes wrong. Step four: program the virtual simulation with huge chunks of code from a video game, which will surely not lead to disaster.
If everything goes right, then the clones will emerge on a distant, terraformed planet, ready to rebuild society. But that's a pretty big "if." Isn't there a simpler way to do this?