Pete insists that the Doctor needs an identity, a human identity along with a complete history. The Doctor grumbles but eventually gives in, muttering about how he should have nicked his counterpart's psychic paper. He takes the name John Smith, but his mother's name is listed as Donna Noble. Partly because if she knew she'd belligerently ask him whether she looked old enough to be his mother with that expression which meant he was going to get slapped no matter what he said. Partly because he wants to remember in some way, because he knows that she won't.
His sentimentality comes to bite him on the arse ten months later when Pete assigns him a secretary because of his refusal to write legible, sensible reports on all the alien invasions he's singlehandedly stopped. Well, almost singlehandedly. He couldn't have done it without Rose, of course.
Pete finally decides that the Doctor needs someone to keep him in line at work and that that someone can't be Rose because she's just as bad as him and they end up snogging next to dangerous alien artefacts anyway. So the unsuspecting Doctor is one day introduced to a loud, obnoxious ginger with a tendency to slap him.
Rose will be the first one to admit that she easily gets jealous and is rather possessive. She's grown out of it, mostly, but it still resurfaces when pretty woman flirt with the Doctor and he cluelessly smiles at them. Donna Noble, however, does not bother her one bit, despite the large amount of time she and the Doctor spend together and the number of times they get mistaken for a couple. She knows that Donna is good for him in a way that she can never be. She never let him go into his spells of brooding and self-pitying, and Rose also suspected that Donna had been giving him relationship advice.
However, both Rose and the Doctor forgot about Donna's file-searching skills. One day, a few months after joining Torchwood, she found John Smith's file. An ordinary person wouldn't have noticed the inconsistencies in his life history, but this was Donna Noble. Not to mention his mother's name. It didn't take long for her to find out that no other Donna Noble had ever grown up in Chiswick in the last hundred years. A little more digging told her that John Smith had never existed until 2008 and that Pete Tyler hadn't had a daughter until 2006.
She learns the whole insane story when she confronts John and Rose. She knew there was something off about these two. Their story makes absolutely no sense, even after Rose explains it clearly after cutting off her boyfriend's high-speed babbling. It takes Donna sometime to process the fact that the person she works for knew her in another parallel universe, shares that Donna's DNA and is also part alien. Oh well, the part alien bit did explain his insanity, though it didn't explain why Rose was insane enough to put up with him.
Rose and the Doctor never get married. It's partly because the idea of Jackie Tyler and a wedding is terrifying and partly because the Doctor insists that he's rubbish at weddings. They do move in together, however, and a few years later Rose gets pregnant with twins.
The twins come into the world screaming. One is a girl whose bright red hair causes the Doctor to tear up. Nobody is sure whether he's jealous or proud. They name her Donna, after the Doctor's best friend in both universes. The boy is dark-haired, blue-eyed and has a charming grin. Rose insists on naming him Jack. The Doctor gives in with poor grace. Jackie cries because she thinks they've named their son after her, and nobody tells her otherwise. The Doctor still grumbles about his son's name, but one night Rose catches him telling little Jack all about Jack Harkness the reformed con man.
Soon the twins are off to school. The Doctor worries because they are geniuses (what else would his children be?) and he doesn't want them to be ostracised because of it. He knows all too well the loneliness that comes with being different. He needn't have worried, however, because Jack and Donna make a new friend on their first day, a little girl named Melody Williams who has bright red curls that explode out of her head, giving the impression that her head is on fire.
Melody' parents, Amy and Rory, quickly become friends with the Tylers. Their first interaction is in the principal's office where they have been summoned because their wards decided to brawl in the playground. Amy is confident, cheerful and flirty, and Rory is quiet with a wry sense of humour. The Doctor, however, suspects that there is vulnerability and maturity behind Amy's confident, playful exterior, and that behind Rory's meek front is a man of steel but also boundless compassion.
Mels, Jack and Donna grow up together, spending more time in detention than in class, causing minor explosions in the Doctor's garage and generally causing a lot of trouble. The one teacher who has anything good to say about them is their English teacher, Miss Oswald, who encourages Mels' writing skills and makes the twins use their brains by making them write their assignments in Shakespearian English.
It's soon obvious to everyone that Jack and Mels are head over heels for each other. Everyone except actual couple, that is. Both the Donnas make it their purpose in life to play Cupid and get them together. Nobody can stand their smugness when they succeed.
Neither of the fathers are pleased with this development. Rory has always been overprotective of his only child and refuses to acknowledge that she is growing up, as many fathers do. With the Doctor, however, it is a different case. He just feels that something is off with their relationship. He thinks Mels is a lovely girl and he's always known that his children would one day grow up and fall in love. But he just gets this weird feeling whenever he sees them together. He tells Rose this when they're making dinner together and she tells him to stop being silly and focus on not burning the potatoes.
He listens to her, because he's long since learnt that she's right far more often than him in everything other than timey-wimey stuff. He listens to his wife (She is practically his wife, even if they didn't undergo the trauma of guest lists and cake tastings) because that's what he does these days. A nine hundred year old Time Lord, living on the slow path, listening to his wife, attending PTA meetings, stopping occasional alien invasion, worrying about his son's girlfriend and still rude and not ginger. He had been running for so long, and then he had been forced to stop. And it wasn't as terrible as he had feared. "It's not so bad," he told Rose. "Stuck with you."