Chiyoko was first seen in an alliance with Axos, who had come to 21st century Tokyo to set up a fake company, which they called the Rising Sun Corporation. One of the corporation's "products" was a drink called "Goruda". Goruda was advertised as a brain tonic, but its real purpose was to transform those who drank a lot of it into Axons. In its public face of "Mr Kin", Axos passed off Chiyoko as "his" ward and advisor.
When Axos encountered resistance from the Eleventh Doctor and his allies, Chiyoko betrayed it, freeing the Doctor's companion, Amy Pond, and Major Harada of UNIT. When the Doctor defeated Axos, the dying gestalt claimed that Chiyoko had promised it the Earth. Chiyoko replied by saying the deception was necessary "for a new life to begin." (COMIC: The Golden Ones)
It turned out that Chiyoko was an evolved amalgamation of the Doctor's TARDIS, Axos, the Shasarak, Konami, Cosette and Margaret Webster. She had what looked like a galaxy on her chest. She destroyed an army of plague robots. She could see through and travel through time through her TARDIS-like qualities. (COMIC: Apotheosis)
After leaving the Doctor and Amy, Chiyoko travelled through time. She freed Axos from the time loop, sent Valdemar to 19th century France and transported the Vorlax Regeneration Drone from 4688 to 2011, setting in motion the events that would lead to her own creation. She went thousands of years into Earth's future and instigated a war between the humans and the Galateans. She was worshiped as a god by both sides. When the Doctor and Amy failed to stop a bomb from destroying the Earth, Chiyoko appeared to them and told them the purpose of the war was to see which race would be the victor. She decided that the Galateans would be allowed to continue and the humans would have to 'go away'. She left Earth moments before it was destroyed.
She later founded the Museum of Lost Opportunities to commemorate the Earth and the human race and to remind herself why the Humans deserved to die.
She was present at the activation of the first Galateans. She put the Doctor, Amy and Alan Turing out of sync with normal time to stop them from interfering. Keltor Jacobs tried to shut down the Galateans. She killed him. She took the Doctor, Amy and Alan to the Planet Kepler IV a thousand years later to show them the extent of the war between the Humans and the Galateans. Next, she took them back to Earth on the day of its destruction, hoping they would die. However, they got themselves Time Scooped back to the Museum of Lost Opportunities.
Chiyoko followed them there and deactivated the Brontë sisters. Before she could kill the Doctor and Amy, the Doctor used the Time Scoop to bring Cosette, Konami and Margaret (from points in their time streams before they were absorbed by the TARDIS) to the Museum. This endangered Chiyoko's existence and greatly limited her powers. The Doctor tried to convince Chiyoko to undo her existence and free the lifeforms she was made of. Chiyoko, who was very regretful, did so.
Before she died, the Doctor took Chiyoko back in time. With Alan's help, he prevented the Galatean rebellion. He uploaded Chiyoko's mind into a Galatean body, allowing her to live safely. (COMIC: The Child of Time)
Later, she apparently joined forces with Josiah W. Dogbolter in an attempt to regain access to dimensional travel. However, it turned out it was actually Frobisher, who used her form as a disguise to distract Dogbolter while the Twelfth Doctor destroyed Dogbolter's corporation. (COMIC: The Stockbridge Showdown)
Chiyoko lived a child's life with her bear Porgy and stuffed unicorns., with Alan and Alan's partner Ranesh on the Galatean lunar colony Athenia. After the Children of Turing began to see Alan as a messiah, he left the colony to work in quiet, giving his whereabouts to Chiyoko but only for emergencies.
Two years later, when the Twelfth Doctor and Bill Potts came to Athenia to ask for Alan's help in translating a mysterious code that had been scratched onto the TARDIS' doors, Chiyoko was immediately aware of the TARDIS' appearance. Feeling the essence of Chiyoko's "mother" the TARDIS on Bill, Chiyoko had Bill take her to the TARDIS, which Chiyoko could hear was screaming due to the markings on the doors. After reuniting with the Doctor, Chiyoko told him where to find Alan. They found Alan inside a replica of King's College, Cambridge on the Moon's surface. The code on the TARDIS was part of the Dreamspace-residing Phantom Piper, and Alan breaking it caused the Piper to manifest. The Piper kidnapped Chiyoko and used her mind, along with the centuries of slaughter locked inside, to bring mathematical constructs of soldiers from every war into existence using Block Transfer Computation. Alan stopped the Piper by breaking down the code that made up the Piper, which freed Chiyoko. Alan then came back to live with Ranesh and Chiyoko. (COMIC: The Phantom Piper)
Behind the scenes
"Chiyoko" means "child of forever" or "child of a thousand generations".