The Noah's Ark Plan (ノアの方舟計画) was a mission carried out in 2055 in response to a destabilisation of timespace as a result of a Third Energy catastrophe.
The etymology of the name comes from the Biblical story of Noah, in which the Jewish God, Yahweh, commands the purest man on earth to construct a vessel large enough to carry all the animals in the known world to survive a flood.
The antecedent to the Third Energy crisis occurred in 2009, in a small republic known as Borginia, located in the South Seas. A Third Energy experiment was conducted that resulted in the manipulation of space-time. The effect "exchanged" space from the distant past, allowing extinct dinosaur species to re-emerge in the wild. The generator was later set to overload, engulfing the facility and everything within its radius to a geographical time-shift - banishing it from the present.
In the 2050s, it was discovered this led to a crack in space-time that began very subtle changes in the flow of history from the Cretaceous Period and the years after. To confirm the effects, a global experiment was conducted to simulated that history after the timewarp. "Distortions" of the fossil record revealed that the cracks had an overwhelming effect on the Cenozoic ecosystem. The conclusions of the research project was that the evolution of human life would be irreparably damaged; wiping out the human race from ever existing.
In 2055, the international organization WAPP declared a plan to repair these discovered anomalies. It was decided that by utilizing Time Gate technology, the living organisms of the Cretaceous could be displaced into a future with a similar environment where they could be unaffected by the alterations - three million years ahead. This would prevent an increase in temporal anomalies from altering -or preventing- human evolution. With the distortions prevented, the team would then return the animals back to their respective times and come back home.
The mission was commenced in August 2055 under the leadership of Colonel Dylan Morton, who had prior knowledge of the outcome of the project from a previous mission with Time Gate technology to the same time back in 2010. Arriving in the future, the team set up an orbital weapons system to help Colonel Morton's younger self.
While these preparations were being made, the MTHR system was entrusted with keeping the animals alive in life-support machines and mentally conditioning them. During its operation, it came to the conclusion that the animals should be trained to follow a 'leader'. Augmenting a Troodon as a test subject, the resulting animal - "Trinity" - was given greater intelligence. It could successfully command packs of Velociraptors.
After an unknown amount of time, the MTHR computer went corrupt and ceased containing the dinosaurs, waking them of their capsules to populate the world. According to the temporally-misplaced people of 2010, the smaller dinosaurs made an appearance first. At time for the team to return, their Gate suddenly destabilized and shut down, preventing them from leaving back to 2055. This resulted in the Noah's Ark team sustaining significant casualties as the animals escaped into the wild, with Colonel Morton's wife Julia being among the dead. A number of children were left alive, albeit injured. They were placed in the very life-support chambers intended for the dinosaurs, to be kept alive while their injuries were treated.
Efforts were made to recover the Gate, but causalities escalated quickly. Colonel Morton's crew managed to fix the Timegate in their last moments, but for one use only. Having prerequisite knowledge of the 2010 criticality, the crew decided that instead of using it to save themselves, they would leave it for their children, in hopes that the 2010 survivors would take care of them.
The chambers would be able to support life and heal any injuries, however, the children would lose their ability to speak. The chambers would teach them things about surviving in this new world and how to coexist with the dinosaurs and protect them, due to the chambers being originally designed for dinosaurs. This would cause problems for the soldiers sent to this time to find out what happened, as the children now had an aggressive goal to protect the dinosaurs from any threats.
The MTHR computer became more and more corrupt, finally going as far as to arbitrarily 'swapping' timespace from the 20th and 21st centuries, dumping the stolen artifacts - from the Statue of Liberty to a US Navy warship - in "Hyperspace", a nexus not part of reality. With the M.T.H.R. computer threatening to cause just as much damage to human evolution as the Borginian anomaly, Lieutenant Morton (Colonel Morton's younger self) was tasked by the Colonel in recruiting someone to travel to Hyperspace and shut down M.T.H.R. That someone was First Lieutenant Mike Wired, an US Army Air Force fighter pilot who died in 1943. It was Morton's intention to displace people moments before their death - that way, if they failed in their mission, it wouldn't matter since the history would record their deaths, anyway.
Lieutenant Wired succeeded in shutting down M.T.H.R. and stopping it from damaging the timeline anymore. Working alongside Colonel Morton's surviving daughter, Paula, Wired was returned to 1943. However, as a 'thank you' gift, Paula displaced the very bullets that were supposed to kill him, thereby rewriting history to have him survive.