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William Hartnell's Doctor was a grandfather, hence from the very beginning of Doctor Who it has always been implied that the Doctor had been a parent. But until Russell T Davies resurrected Doctor Who in 2005, there were never clear hints to the Doctor being a father. Steven Moffat's very first Doctor Who episode, "The Empty Child," first mentioned the Doctor as a parent when the Ninth Doctor (Christopher Eccleston) and Dr. Constantine (Richard Wilson) commiserated both losing children and grandkids in battle.
The Tenth Doctor (David Tennant) offhandedly referenced being a father in Doctor Who season 12, episode 11, "Fear Her," although he never elaborated. Years later, in Doctor Who season 7, episode 7, "A Good Man Goes to War," Matt Smith's Eleventh Doctor declined to respond whether he ever had children. It is consequently generally agreed that the Doctor had offspring probably murdered or lost in the Time War. The Tenth Doctor essentially verifies this in Doctor Who season 4, episode 6, "The Doctor's Daughter," when he says:
I perceive them. All the suffering they left behind filled the hole. Simply said, I'm not sure if I could handle it daily.
Further attesting to this in Doctor Who season 8, episode 12, "Death in Heaven," Clara Oswald (Jenna Coleman) passed for the Doctor. Beside Cybermen, she claimed that following the Time War the Doctor's children and grandchildren were gone, thought dead. Furthermore mentioned by Clara was the non-Gallifreyan child born by DNA transfer—Jenny (Georgia Moffet). Finally, the Fifteenth Doctor tells Ruby Sunday (Millie Gibson) that he had children and a granddaughter in Doctor Who season 14, episode 2, "The Devil's Chord," which is why his disclosure regarding Susan's parents seems so odd.
Russell T Davies couldn't resist muddy the waters when it comes to the Doctor's children, even for all the riddles season 14, episode 7 answered. Inquiring about his granddaughter from Kate Lethbridge-Stewart (Jemma Redgrave), the doctor notes he does not yet have children. From a linear point of view, this is a reversal of what has hitherto been known about the Doctor's offspring; but, given the Doctor is a Time Lord, linear viewpoints never fully tell the story. The conversation between Kate and the doctor hints on how both things might be true:
Kate: You mean, you may have a grandchild before a daughter?
The Doctor: Time Lord Life...
This disclosure suggests that a future Doctor might settle down and start a family; one of their offspring goes on to be Susan. The Doctor's life would thus be a closed loop, with some event returning Susan to the beginning of her grandfather's trip across time and space. Doctor Who is quite unlikely to ever unveil Susan's parents or the mother of the Doctor's offspring. But like Trenzalore in the Steven Moffat era, the birth of the Doctor's children might serve as a set terminus for the narrative of The Last of the Time Lords.
Whether her roots are timey wimey or not, the Doctor very certainly left Gallifrey with Susan Foreman, his granddaughter. Traveling together, the Doctor and Susan finally split when she was left on Earth to assist in reconstruction following a Dalek invasion in 2150 AD. The Doctor decided to leave Susan behind as David Campbell, her partner, could provide her granddaughter a stable life. With spinoff media suggesting numerous other hypotheses, several stories have called into doubt Susan's even biological granddaughter status.
Originally written by then-script editor Eric Saward, the 1983 short story Birth of a Renegade exposed Susan's ancestry as Rassilon, the creator of Time Lord society, According to this story, Susan was taken from Gallifrey by the Doctor in order to hide Rassilon's political rival. Though part of an official product, the Doctor Who 20th Anniversary Special—written by Doctor Wh's script editor—has been overlooked by canon. Doctor Who season 14's references to Susan unequivocally establish her as the Doctor's biological granddaughter.
The Doctor also has a verified daughter, Jenny, produced on the planet Messaline by use of clone technology. Their progenation machines could create full-sized people to assist in their ceaseless conflict with the Hath. In that regard, the Gallifregyn looms from expanded media resembled the progenation machines in Doctor Who season 4, episode 6, "The Doctor's Daughter". Gallifreyan infants are genetically "weaved" on enormous looms, not created by biological reproduction, according to Marc Platt's several Doctor Who books including Cat's Cradle and Lungbarrow. On-screen confirmation of this reality has never come about, though.
Although the Tenth Doctor first battled to accept his replicated daughter, he and Jenny bonded at last. Tragic events happened, and the ever deranged General Cobb shot Jenny. The Doctor disagreed Jenny could regenerate since she combined human DNA with Gallifreyan. Consequently, he, Martha Jones (Freema Agyeman) and Donna Noble (C Catherine Tate) abandoned Jenny's remains to be buried on Messaline However, Jenny was able to regenerate to an extent that healed her wounds, and she set out across the stars to be a hero like her father. Jenny, the daughter of the doctor, was a cherished character since she was the only one child. Jenny has never returned in Doctor Who, though.
In "The Devil's Chord," episode 2 of Doctor Who season 14, the fifteenth doctor suggested that the Master's slaughter might even have impacted Time Lords not on Gallifrey at the time. This would mean that following the events of "The Timeless Children," any of the Doctor's children—past, present, future, or otherwise would be dead. But Jenny, the Doctor's daughter, would have avoided this destiny since she is not totally Gallifreyan. Given Carole Ann Ford left the show long before Time Lord biology was even considered, Jenny might even prove to be Susan's mother further down the road.
Jenny is therefore the only child of the Doctor who still lives in the Doctor Who world. Tragically for both characters, the Doctor's daughter has no way of locating her father down as he never remains in one location and time for long enough; the Doctor isn't even aware Jenny's still alive. Regarding the Doctor's granddaugher Susan and her parents, they remain missing assumed dead after the twin tragedies of the Time War against the Daleks and the Master's genocide.
For Doctor Who viewers, the riddles about the Doctor's offspring have always piqued their curiosity. While also casting doubt on the Doctor's background and his relationship with his family, the disclosure that he has children and a granddaughter gives his narrative still another level of complexity. The fourteenth season of Doctor Who has carried on examining the Doctor's relationship with his granddaughter Susan and included a new character, Ruby Sunday, who also seems to have links to the Doctor's past. Fans in the next seasons will continue to find great fascination in the issues of Susan's parents' identity and whether any of the Doctor's other offspring are still alive.
Along his trip across time and space, the Doctor's family has been very important. Their presence—even in absence—shapes the Doctor's perspective of the cosmos and his goals. Examining the Doctor's family in Doctor Who gives the narrative of the show a fresh angle and helps one to better grasp the Doctor's character and his place in the great sweep of time and space.