Hybrid Incident

The Hybrid Incident was the Time Lord designation for the event in Davros attempted to create the Hybrid on Skaro. (TV: The Magician's Apprentice/The Witch's Familiar, PROSE: Dalek Combat Training Manual)

A day to come
Through the projections of the Matrix, the Time War-era Time Lords learnt that the Twelfth Doctor had tried to demonstrate mercy to a young Davros. Through this, they saw that he had shown some way of circumnavigating the Blinovitch Limitation Effect, allowing him to return to an exact space-time event multiple times and influencing the outcome of that event. Investigations were undertaken as to how the Doctor was able to achieve this, and discussions took place at High Council level to determine whether they constituted a breach of the First Law of Time. The Time Lords believed that the Doctor had failed in his mission, as they could find no evidence that any Daleks in their current relative time zone had any understanding of mercy. (PROSE: Dalek Combat Training Manual)

The Incident
While looking for a bookshop, the Doctor found himself on a battlefield during the Thousand Year War on Skaro, and encountered a young boy trapped in a field of Handmines, and, during the rescue attempt, learned that the boy was Davros. When he "should have been brave enough, [and] strong enough to do something better", the Doctor fled the battlefield, unwilling to save or kill the boy who would create the Daleks. (TV: The Magician's Apprentice)

Having somehow survived the fall of the New Dalek Empire, (PROSE: The Whoniverse) Davros, on the brink of death, remembered his encounter with the Twelfth Doctor in his childhood, and ordered Colony Sarff to bring him to him "while there [was] still time". (TV: The Magician's Apprentice) The Doctor prepared a confession dial to be delivered to, aware that she had escaped her apparent death at the hands of the Brigadier during the 3W Institute Affair, and went to the planet Karn to meet with Ohila and the Sisterhood of Karn. After hiding from Colony Sarff behind a rock, (TV: The Magician's Apprentice) the Doctor was told by Ohila that he owed Davros nothing by partaking in a confrontation, warning him his actions would spell his end. Giving Ohila his confession dial before departing, the Doctor proclaimed that he would find a rock to meditate on in preparation for his possible destruction. (WC: Prologue)

Travelling to Essex in 1138 A.D., (TV: The Magician's Apprentice) the Doctor gained a servant in Bors when he removed a splinter from him. After three hours of meditation in a castle, (TV: The Magician's Apprentice) during which he thought back to his previous incarnations, (PROSE: Full Stop) the Doctor decided he needed better drinking water, and gathered the locals to dig a well. After eleven days of finding a supply of water, and another day to construct the well, the Doctor, rather than resume his meditation, decided to make improvements to the castle, such as adding a sunroof to the throne room, (TV: The Doctor's Meditation) building a first-class, child-friendly visitor centre, teaching the locals mathematics and introducing the word "Dude" to the 12th century. (TV: The Magician's Apprentice) While additions to the throne room went underway, the Doctor had a conversation with Bors about him avoiding his meditation. Four days afterwards, the Doctor finally decided to begin mediating again before leaving the next day, and also divulged to Bors the reasons he had for being reclusive. (TV: The Doctor's Meditation)

Receiving the Doctor's confession dial from Ohila, Missy tried to find the Doctor to get answers, but was unable to locate him. Needing assistance, Missy got the attention of both Clara Oswald and UNIT led by Kate Stewart, whom last saw her during the 3W Institute Affair, by freezing all the airborne planes on Earth in time. Managing to arrange a treaty with Clara, Missy helped UNIT deduce that the Doctor was hiding in 1138 Essex, and used her vortex manipulator to transfer herself and Clara to the location, where the Doctor was throwing a party.

For his last day at the castle, the Doctor decided to have an axe fight with Bors, and arrived on a tank playing an electric guitar. While trying to get the crowd to understand his jokes, he realised Clara and Missy had tracked him down, whereupon Bors was attacked by Colony Sarff, who demanded that the Doctor attend to Davros. Reminded of his shame at leaving the young Davros behind, the Doctor reluctantly agreed to go as a prisoner, with Clara insisting she and Missy be taken prisoner too. Sarff brought the trio to Davros' infirmary, where he was dying. While Clara and Missy were left in a cell block, the Doctor went to see Davros, who revealed to the Doctor that they were on Skaro. On a monitor, the Doctor saw that Clara and Missy had escaped their cell and been captured by the Daleks, who had also procured the TARDIS. Missy was seemingly exterminated as she tried to convince the Daleks to work with her, with Clara quickly being exterminated as well and the TARDIS was seemingly destroyed. (TV: The Magician's Apprentice)

In what one account described as "the Last Night" of Davros's life (PROSE: Davros, Dark Lord of Skaro) and when he faced the Doctor again, Davros talked about the Daleks, calling them children. He admitted that even though he created them, he could not control them, claiming he could not stop them from exterminating the Doctor's friends. During this meeting, Davros showed the Doctor that he had recorded all his foe's speeches about morality. Perhaps as a taunt, Davros singled out one about killing a child who would grow up to be a "ruthless dictator who would destroy millions of lives"; the Doctor had the chance to prevent Davros from ever creating the monster known as Daleks, but had failed because of his compassion. (TV: The Magician's Apprentice)

Davros revealed the cables connected him to the life force of every Dalek. While attempting to make the Doctor feel compassion for him as part of a plan to steal his regenerative energy, Davros learned that the Doctor had saved Gallifrey from destruction at the end of the Time War. Whether sincerely or not, Davros congratulated the Doctor on saving his people, referring to his own failure to save the Kaled race from extinction. Shutting down his ocular system, Davros told the Doctor that he wanted to see one last sunrise with his own eyes. However, when the Doctor, apparently driven by compassion, released regenerative energy into the cables, Davros was quick to act; using Colony Sarff to secure the Doctor, he began siphoning regenerative energy from the Time Lord and transmitting it into every Dalek across Skaro, using some of it to renew himself and remove his reliance on the life support for survival.

However, after being saved by Missy, the Doctor revealed that he had known of Davros' plan, and had let him take the energy as part of his own plan to stop the Daleks. He then revealed that Davros' transmission of the energy into every Dalek on Skaro had included the decaying Daleks in the sewers beneath the Dalek City, who attacked and destroyed it, with Davros still inside when the roof of the infirmary collapsed on him whilst the Doctor took his leave with Clara. Missy, meanwhile, found herself surrounded by Daleks in the crumbling city, only to announce that she had a "very clever idea". (TV: The Witch's Familiar)

Davros and the Daleks
Having survived the incident, Davros recorded a "whole and true study" of Dalek history and science to ensure their purity and survival in case he ever died. In this study, he wrote that he was still connected to the life force of every Dalek, but that he had the stolen regeneration energy, making him question what may be possible in the future. He concluded his discussion by once again stating that his children were the ultimate form of life and that all other lifeforms needed to be exterminated. (PROSE: Secrets of the Dalek Laboratory)

The Doctor and the Hybrid
The Doctor resumed his travels with Clara. Along the way he encountered the part-human part-Mire Ashildr (TV: The Girl Who Died, Hell Bent) and the simultaneously-human-and-Zygon Osgood, both of whom he identified as hybrids. (TV: The Zygon Invasion) On Gallifrey, which had discretely returned from its pocket universe to the end of the universe following the so-called fall of Gallifrey, Lord President began to fear that the fall that the Visionary had foreseen would be brought about by the Hybrid and began researching the creature. Possibly due to being influenced by Missy, Rassilon came to believe that the Twelfth Doctor held the information he desired. Ordering the death of Clara Oswald, Rassilon trapped the Doctor in his confession dial to get information out of him. (PROSE: A Brief History of Time Lords) To this end, Rassilon contacted Ashildr to have her assistance in the kidnapping of the Doctor, (TV: Face the Raven, Hell Bent) and trap him within his own confession dial in an attempt to learn everything that he knew about the Hybrid. The Doctor's refusal to relent led to his being trapped inside the dial for four and a half billion years, constantly dying and recreating himself to breach the dial's barriers rather than confess his secrets. (TV: Heaven Sent, Hell Bent)

On his escape, the Doctor finally returned to Gallifrey, (TV: Heaven Sent) where he banished Rassilon before embarking on an effort to save Clara's life. In the Cloisters at the end of the universe, Ashildr posited to the Twelfth Doctor that the Hybrid could be interpreted as referring to more than one being: specifically, the pairing of the Doctor and Clara. Just prior to losing his memories of Clara, the Doctor indicated that his reckless actions in trying to prevent her death made him the Hybrid. (TV: Hell Bent) A Time Lord author agreed with this theory, noting it was the only one that truly fit the prophecy. (PROSE: A Brief History of Time Lords)

Missy
Missy remained on Skaro for a time, adopting a Slyther as a pet. She named it Doctor and allowed it to eat the Thals she came across. (PROSE: Postcards from the Universe) Eventually, she escaped the Daleks using "a teleport, stairs, three bald lies, a classical ballet routine, and a leap into the Time Vortex", only for her TARDIS to end up in a temporal embrace with a Gryphon space-time vessel. There, she was surpised to learn the captain had no knowledge of the Dalek Empire, yet she dropped the subject. (PROSE: The Liar, the Glitch and the War Zone) Missy eventually came across the Doctor again when she was subjected to the Fatality Index. During this encounter she stated that the "word among the Daleks" was that the Doctor had retired to "domestic bliss" on Darillium. (TV: Extremis)