- "I'm going to change history. I stared at the darkening skies above me, and steeled myself. I will succeed."
- — Sigma, on saving the world from Radical-6
The headquarters is a very small room with little in it. A small antique TV sits in one corner of the room. Nearby, there is a small window cut into the wall, which gives a view of the city's expanse. It is currently unknown which city it is in. Three treatment pods are lined along the wall. They contain the frozen bodies of Clover, Alice, and Phi. A single light bulb dangles from the ceiling. A wooden door leads out of the room. The walls and floor are a grayish color.
End or Beginning?
After supposedly being stabbed by Akane in January 2074, Sigma's consciousness transfers itself back in time 44 years, to April 13, 2029 inside of this room. A TV turns on, a news report running on it. The reporter talks about the destruction caused by Radical-6 and shoots herself in the head with a gun. The connection is cut, and Sigma hears footsteps approaching behind him.
He turns around and sees Zero in a Free the Soul robe. Zero takes off the mask and Akane is revealed to be underneath it. Sigma comments on how she killed him in 2074, but it turns out that she hit him with the handle of the knife in order to get him to jump through time. Akane says that he is in her headquarters on April 13, 2029 and they are about to leave to Rhizome 9 the next day, carrying three treatment pods with Alice, Clover, and Phi cyrogenically frozen inside of them.
She tells him that after they get there, he will spend the next 45 years mastering genetic engineering, creating Kyle, Lagomorph, and Luna, develop the technology needed for the game (the Chromatic Doors and bracelets), and bring Tenmyouji and Quark to the facility in 2074. After all that is done, his consciousness will go back to December 25, 2028 to successfully stop Radical-6 at the Mars Mission Test Site in Nevada. She also tells Sigma that the Mars Mission Test Site is full of traps and that Sigma lost his arms and an eye by trying to save a woman's life.
The reactors suddenly explode and she prompts Sigma to look outside the window. He sees a huge mushroom cloud enveloping the city and vows to himself that he will stop Radical-6, no matter what.