3-5 Main Story: Birdcages (Library Summaries)

1
Having been tasked with repairing a satellite that connects Earth and the moon, a brother and sister descend into a relay server.
There, they find many paintings adorning the walls—it's like a museum.
Among them is a painting of a dragon impaled upon Tokyo Tower.
The plaque says that this happened in 2003, but neither brother nor sister remembers it. But they both know it is no ordinary painting. And so, they press on to solve the mystery.

Suddenly, a white substance begins to fall and builds up on the floor. It is not snow but fine pieces of salt.The footprints pressed into the salt are not human.
The siblings follow the footsteps, only to be attacked by a monster with red eyes. Brother and sister, who once hated each other to the point of killing each other, now protect one another, parrying the monsters clumsily with their swords and press onward.

The salt comes to a stop, and the two find a new painting. It shows how the salt-borne disease wrought by the dragon's death turned regular people into red-eyed monsters. They recognize that this story is one of a world very similar to their own. Several different worlds exist, split like a branch upon possibilities. The world they see is one that lived through a nightmarish history.

2
Brother and sister come to an old-fashioned gallery where they encounter a pale aberration. It speaks like a broken machine, but it shows them no malice; it's almost as though it's there to greet them.

The aberration guides them through the facility, and they witness the history of the world in which the dragon appeared.

"The Soldiers Who Fight the Monsters" showed that those who fought against the red-eyed monsters formed a military organization called the Crusades and sent an endless stream of young people into battle. Among these children, they find a brother and sister who look exactly like them.
They fought, ran themselves ragged, and countless many died.

"Humanity Revival Project" showed those who desperately searched for a way to escape the salt-borne disease. There, technology to split the human body and soul then preserve both until the right time came, all to stop the progression of the disease, was born.

"The Extinction of Humanity" showed the end of all things.
No matter how many monsters they fought, no matter what technology they developed, humanity understood there was no escaping their demise. And so, they turned to their final option. They left the key to humanity's revival for the far distant future.

They locked away the human genome and all of humanity's culture, history, and memory into The Cage. But now, the enemy is destroying The Cage.

3
The girl stands in the Bunker's command room.
This was the androids' base for their fight against the machine lifeforms that encroached on the Earth—weapons unleashed by the aliens when they landed in the year 10,000.
The girl herself was once among them. But with the end of the war comes a machine attack on their base.
Elite soldiers infected with a virus appear before her.
This virus, built to destroy androids, spreads in an instant. The girl avoids her old android friends as they brandish their weapons and yell at her, welcoming her back to her home. She makes her way through the base to see if any are safe.

The girl finds a single sword in the corridor. A voice floods her mind the moment she lays her hand on it. She learns that its old wielder, too, lost her life due to the virus. There are no more sane androids; the base has been annihilated.

Her home gone and missing her friends, she has no choice but to endure by tricking herself into thinking she is used to being alone. Her heart, too, has lost its home. "Maybe I should...join everyone..." she murmurs as she listlessly walks the corridors.
Black birds appear from thin air and gather around the weakened girl, forming a black sphere. The sphere shoots into the air, leaving this world.

4
The siblings stand in an inky black darkness. If they manage to restore this last access point, then the path to Earth will be opened.

As their eyes adjust, they proceed upwards around the outside of the tower. There, they find an old, run-down device resembling a projector. They activate it, and it displays hologram data. It is a record of the war between the androids and the machine lifeforms.
It is a long history—one that will lead to the machines' eventual rule over every city... The completion of their kingdom.

The top of this tower is familiar. It is the altar at which the two of them restored the broken sun and moon. But what comes to mind for both are memories of destruction. They invited the enemy into The Cage to make their wishes come true.
Even as they fight the enemy, their hearts are tainted with despair.
But the encouraging words of the friend who sent them here flash through their minds, and that alone is enough to make their hearts one.

Sun and moon meet to form an eclipse—the true gate that links Earth and The Cage. But at the same time, the enemy attacks to close the gate.

Behind all of those who rush toward the gate, the android girl stops to keep the sun and moon from separating. She knows she is breaking due to the infection, and so she has thrown her own life away for the sake of the friends who saved her from loneliness.

"We didn't have much time together, but I had a lot of fun," she says, her words skipping and glitching, despite knowing they will never hear her.

And so she leaves the fate of The Cage and Earth to all her friends.