3-6 Main Summary

1
Pod activates the device, which connects to a memory of when the quantum server on Earth was in operation.
The memory shows the past of a boy and girl, both clad in white.
They are the administrators of the quantum server, and they have no names.
They are only called Him and Her.
Theirs is a simple role: to observe all the memories of humanity recorded in the server. They venture through the server's virtual space.
He encourages Her to activate the device, which then connects to a memory of long, long ago.
It is a time when human science made significant advances and culture flourished. It seemed the device could draw up memories recorded in the server.
She accesses more and more and sees what becomes of humanity.
She comes to know their future, the pain that plague and violence causes them, and their trudge toward extinction. While She grieves humanity, He speaks of His belief that they will be revived one day.

2
Pod accesses the next device.
There, they see a memory of what happened after the quantum server deteriorated. Inside the broken virtual space, the Red Girl accesses a crumbling device.
It is a memory of when humanity had gone extinct and their cities crumbled...a time when the Red Girl commanded the machine lifeforms in their conquest of Earth and waged war with the androids.
While the machines had the upper hand for some time, the war ended with both sides suffering heavy losses, neither side the victor. The Red Girl, too, was at the end of her life. She incorporated the machines' memories into herself. She burdened herself with their pain and suffering in hopes of expiation. As she continued onward, She appeared. The Red Girl then reaches out to Her, though She is meant to be her enemy, and pleads for salvation.
The last thing the Red Girl speaks of is her loneliness.
But She absorbs the Red Girl and then uses her power to transform the city.
In the end, it looks just like The Cage.

3
The device in front of The Birdhouse connects to a memory of when the quantum server was established.
He was created within the server to observe humanity's memory.
The first thing He sees is humanity's grim path to extinction.
He attempts to save people, but He cannot interfere with memories.
And so, He decides to incorporate the memory into himself, believing that knowing their pain and suffering would make salvation possible.
But the server not only houses memories of the past but the future as well.
After watching memories of the lifeless dolls' war, He sees a future where Earth is a series of strange buildings. And then, He watches His own birth. History repeats itself. As He watches history run the same path over and over again, He learns of human emotion, and He finds pain in His loneliness.
And so He births Her, believing He can change His own fate.