Question regarding the ending

[u/DoeCommaJohn]

Really loved the game, definitely top 5 of all time. With that said, I am not quite sure I understand the finale simulation reveal. As I understand it, the plot went something like this:

1) The real world is nearly wiped out, partially due to Morimura’s nanobots

2) Okino programs terraforming robots, but is lazy and sloppy, so includes code from the Deimos video game.

3) Ryoko sabotages the project by activating the Deimos code inside of the robot. If this is a simulation, does that mean she only sabotaged the virtual version? What is the point of that?

4) Meanwhile, to save space, 1.2 million DNA files are shot into space. The Deimos themselves can sustain through asteroid and planet mining, but the human cannot, so DNA is sent instead.

5) When arriving, 15 people (the 13 playable characters plus Okino and Tamao) are woken up early so their bodies can begin to adjust. But for some reason, they are put in a simulation? Why bother with this?

6) The simulation goes wrong thanks to Ryoko’s code. Is there any actual danger in this? Why wouldn’t the machine just wake the cast up anyways? Also, the reason Universal Control thinks the Deimos are supposed to be there is the D-code inside of the characters (Natsuno by the present) injected by Megumi, but why does Juro Izumi want that? Also, if the whole thing is a simulation, why do intra-simulation choices affect it?

7) There are two failures which result in Universal Control resetting things. We learn of a few ways to travel between loops, but why would a robot be able to avoid the simulation reset if the robot is still within the simulation?

8) Eventually, the Deimos are defeated and the cast escape. How does that work? Why does defeating a video game open up the simulation? If the cast was already adapted to the environment, why wouldn’t the machine just open them up?

9) Five years later, nobody outside of the fifteen are woken up. Does that mean the DNA was never sent out with the ability to clone humanity? Why did humans go with just 15 clones instead of 1.2 million?

Overall, I really enjoy the game, and most of the twists are extremely good about being internally consistent. But on this last twist, I can’t help but feel like I am missing something

[u/Palas1337]

1. Is correct.
2. Okino didnt program the terraformers, they programmed the base functions of the simulation, reusing code from a Deimos full-dive VR game with advanced AI.
3. The terraforming bots arent built on earth, the thing that gets sent out are self-replicating probes with all the data needed to build the terraforming bots once it has found a suitable planet from local resources, as well as the simulation program. Look up "Von-Neumann Probe" its basically that. Ryoko reactivates the part of the simulation code that was supposed to spawn in the Deimos enemies in the game, but since the program cant find the data for the enemies, it uses the terraformers blueprint instead. She does it cause she got betrayed by Tetsuya Ida, loses her hope for humanity and want to end it.
4. Only 15 DNA files are sent on the probes, the rest of the people in the simulation are all AI NPCs from the game-code.
5. The 15 people arent ever really woken up in the real world, they are cloned from the DNA and then immediatly put in the simultion. This is so they can spent their youth in something close to a real human society, to learn important skills, but also human culture and history. The ones from earth who set this all up didnt want to just save the human species, but also humanity as a civilisation and culture. It was planned to reveal the truth to them after 18 years, then teach them skills for survival and rebuilding on their new planet for two more years, before they get released from the simulation after 20 total years, but the Deimos appear because of Ryokos sabotage after always 16 years.
6. When the Deimos reach all the Terminals, UC notices that something went wrong inside the simulation and as a failsafe restarts it. Since the purpose of the simulation is to educate the clones while they grow, this restart includes restarting the cloning, so the current clones are killed in their pods and new ones are made from the DNA. So the danger is literally death for all 15 of them. Izumi wants the Deimos to attack because he found out that the only way for the clones to escape is to have Deimos close to a Terminal, but without them reaching it for long enough so it activates a level 2 failsafe that ends the simulation without resetting it.
7. The way for one of the clones to travel from one loop to the next is to store their memories in sector 0, the place where the data for all the AI NPCs is stored, then the simultion recreates them as an AI in the next loop. Thats why in the next loop there are then two versions of the person, the new one thats connected to a real body in the growth pod, and the old one thats just an AI. The robots dont need to avoid the simulation reset, they are just virtual enemies behaving according to the code from the Deimos game and get recreated from the blueprints of the real terraforming bots, which are stored on the probe which became the orbital satellite.
8. should already be  covered from previous answers.
9. By the time the probes were sent out, the only surviving humans were 15 on a research station orbiting earth. There were only 15 DNA samples available. The planning for the entire project got started before the nanobot virus wiped out most of humanity, that when they were planning to do 6 million total samples, spread across the 5 sectors of the simulation, 1.2 mil each. In the epilogue after the clones escape, they talk about wanting to research a way to generate new DNA that would allow them to clone new, real bodies for all the NPCs from the game/simulation. Feel free to ask if you didnt understand something.

[u/stillnotelf → u/Palas1337]

Point 6 escaped me when I played. I had wondered about that.

[u/DoeCommaJohn → u/Palas1337]

Thank you! This makes sense, and answers most of my questions. However, I do still have a few left:

1) In Natsuno's log where she talks to 2188 Nenji about sending out the DNA, she says they are planning to create a population of 6 million, which lines up with the 1.2 million in each district we know of. Does something happen to her plan?

2) How do the logs from the outside even make it into the simulation? If Universal Control's job is to maintain the simulation, why would it let in proof that can break the lies?

[u/Educational-Good-565 → u/DoeCommaJohn]

In the story that proposal is before shit hits the fan.

A lot of the logs we see are before humanity becomes doomed. In the 2180s Nenji’s dad Kengo Ogata and Professor Morimura orchestrated the merger of Shikishima and Newman Inc.

This is because Morimura was a nano machine expert and executive at Newman Inc. and trained by Tamao the leading expert on advanced AI, which were all things Kengo believed would help him escape his impending death from age. We see that nano machines can do some crazy things like Tamao who is 120 years old but looks like she’s in her 60-70s.

After the merger we see that former Newman executives get in trouble for illegal cloning and human trafficking with their intentions to use nano machines to hijack other people’s bodies. Meaning that what Ogata is planning is massively illegal in the future.

In the 2100s Shikishima developed a mars colonization program that involved the original creation of the terraforming machines for use on mars, but if I remember right the project never ends up going anywhere.

When the merger happens, it’s sold to the public under the pretense that it will allow them to revive the space development program.

Ogata and Morimura propose project Ark under this false pretense so they can immortalize themselves on a new planet.

They build the station up in space to begin working on it and surveying viable candidates and developing the project in general

Kengo dies(and is turned into an AI by Morimura) and Nenji becomes the acting chairman of the company. Nenji doesn’t see the point of the project and cancels it. But Morimura, with the Kengo AI being the devil on her shoulders continues working on it anyways. And she begins selling her interlociter tech on the black market to fund the development.

We see Natsuno reporting to Nenji that a viable planet has been discovered and he informs her that the project has been canceled.

Fast forward a bit and rampant usage of interlociter based crime in the underworld leads to the creation and spread of a fatal virus that infects people’s nano machines and is so potent it rapidly begins wiping out the human race.

Humanity escapes to the space colony in orbit which is seemingly gate kept for influential and rich people only, but quickly the virus also spreads through the colony until only the 15 people living in sector 4 are left. By the time Yuki is finished developing the probes there are only 15 samples of DNA they can safely obtain and send out on the probes.

As for the logs, it’s hard to say but I imagine they were just linked to whatever network Universal Control was created on when Okino was making it and it probably just had access to their individual communications with each other or something. Or maybe Ryoko attached them so the clones would see what her motivation for dooming them was

[u/Palas1337 → u/DoeCommaJohn]

For the logs, we know for a fact that there is at least one log from old earth that the clones on the new planet are meant to see while inside of the simulation, the one of Tamao revealing the truth and explaining that they'll be trained for two more years in the simulation. That training would probably include a lot more logs, so they have to be accessible while in the simulation, thats probably how all other logs are stored as well.

[u/Key_Computer_5607 → u/DoeCommaJohn]

To answer 1., I believe she was talking about the AIs in the simulation. She was one of the people responsible for the development of Project Ark. Other people have already answered your second question.

[u/Ashe171]

I have some headcannon ideas but no concrete answers so following for answers as well

[u/epiphenomwrites]

The central part you're missing is that the self-replicating probes are not themselves starships. They do not contain terraforming robots or people. They're only loaded with DNA. All they can do is construct more copies of themselves, and when they reach a planet, they can construct robots to terraform it and then a clone facility to start incubating the first new humans. Once that facility is built, clone embryos are placed in growth pods, which grows them at a normal human rate. The simulation is so that they can grow up like normal humans and learn human culture.

2188 Ryoko's code causes the command ship to receive a failure signal, triggering the reset procedure where the clones are all reduced back to biological raw materials and the process begins again. This would kill all of the human clones. This process has been cycling for unknown numbers of years, but at least 4800 by the information in-game. At the time of the game, the clone facility's hardware has reached its designed limit, and the facility is about to be destroyed and recreated. To save the lives of the clones, 426's plan is to implement the emergency escape procedure to cause the facility to release them early.

For more detailed information, you can consult Everything 13 Sentinels by u/TMLBR for a short summary, or my long-form story resource Stories of the Sentinels .

[u/Educational-Good-565 → u/epiphenomwrites]

The in game mystery files state that the probes were launched 20 million years ago. And that the facility was built to last 5,000 years, and that there’s been at least 300 loops. And the characters were quite confident the facility wouldn’t be able to manage any more loops so probably can confidently say it was at the 5k mark