The loops were not part of the plan for Project Ark. Project Ark was supposed to commence growing these 15 people in the pods after terraforming of a suitable planet had completed, using the preserved DNA from their 2188 counterparts who were the last remaining humans on the space colony after a deadly nanomachine plague/virus had wiped out nearly all of humanity. It was supposed to have them live in these simulated time periods from 40-year eras of modern history prior to when things hit the fan in the 2100's with the nanomachines apocalypse. They were to learn about human life throughout this simulation (which they would believe was real) before being released from their pods at the age of 18. Once released, they'd spend two years in the facility that had been built and maintained on a satellite orbiting the terraformed planet (built by the probes that endlessly self-replicated and searched the galaxy for planets suitable for terraforming) learning about how to commence fleshing out the planet with flora/fauna and growing the human race anew.
So that was the plan.
- 2188 versions of the cast of characters developed Project Ark
- Project Ark sent out self-replicating space exploration probes carrying the DNA of themselves and two others (Okino and Tamao).
- These probes travel for upwards of millions of years across the vast expanse of space to find suitable planets.
- Once any one of these replicating probes found a suitable planet it would commence producing the terraforming machinery (which you see in the simulation as the "kaiju") and terraforming the planet. This process takes like 1800 years I think.
- It would also construct a facility to house the pods, resources that would be used to populate the planet after terraforming, and the computing devices used to run and maintain the simulation that all 15 clones (in their pods) would be experiencing
- Once they grew to the age of 18 within their pods, they'd be released and trained for two years within the facility by video logs and such on how to go about setting the planet up as a new Earth, essentially.
- Since they would've lived through this simulation for 18 years, they'd have an understanding of what human life was and what it could be rather than just being born onto this new planet as animalistic beings with no sense of humanity or connection to humankind's past.
Buuuuuut Shinonome (2188) was pretty much done with humanity due to depression, cynicism, and feeling betrayed by 2188 Ida, whom she loved. So she quickly altered the simulation to have the terraforming machines manufactured and released into each sector, destroying everything in their path on the way to that sector's mainframe terminal. Since 2188 Okino cut some corners when designing the simulation by using code from a Deimos game to handle the environment generation/simulation, Shinonome was able to tap into that quickly and used instructions to reach out to the satellite orbiting the planet undergoing terraforming to use the terraforming machinery as the assets that would serve as the "kaiju" because they were large, destructive, and already existed within the code. Once all five sectors' terminals had been breached, the simulation would automatically reset and rebuild everything from its original starting point, basically breaking down the existing 16-year-old clones in their pods and rebuilding them anew as well. So basically she felt that humanity was doomed and wanted to prevent it from having any chance of surviving Project Ark. She set this protocol to execute every 16 years, ensuring them the pods would never be able to release the 15 clones at the age of 18 as intended.
The facility that housed the pods and ran the simulation was nearing its breaking point in terms of stability, which according to the Mystery Files suggests that it had been stuck in loops for about 5000 years after the terraforming of the planet completed the the pods started growing the clones. This means that about 300 or so loops had occurred before this crew finally managed to break free of them by alerting the simulation to the presence of the "kaiju" and allowing it to purge them without rebooting and starting yet another loop. So the stakes were actually pretty high here as the facility would've probably broken down within another loop or two, and then Project Ark would've been a failure. Well, at least this one instance/planet of Project Ark. 😉