He never intended to pick her as a companion, but when he thinks about it, when did he ever intend to do anything? She's mousier than most, seemingly not a fighter, but she's clever and she stays where she's told and so help him, she belongs on the TARDIS.
"What are you?" She asks incredulously, wandering around the control deck with wide eyes. It dawns on him that's the first time anyone's skipped straight past the basic introductions; already he's fond of her.
"Good question. Not human. I'm the Doctor."
She gives a small laugh. "Right. Course. Can't shake them, me." He shoots her a quizzical look, and she hurries to add, "Molly Hooper. I work at the morgue in St Barts Hospital in London?"
"Ah, excellent! Now, Molly Hooper of St Barts Morgue, where would you like to visit first?"
-:-
There's no need for introduction with her. They visit the Triplet Lungs on Garthenfret in the beginning, two days before its implosion, and she's awed by it. There's no other word for it – her astonishment is tangible. She doesn't want to leave (when do they ever) but she doesn't kick up a fuss or flat out run off. Instead, she ambles back to the TARDIS, talking a mile a minute. The Vaalens – a generally friendly tribe of water-dwellers, native to Garthenfret – assume she's prey and before the Doctor can even begin to save her she's flung the ringleader into the distance and is watching in thinly veiled satisfaction as the rest of them disperse.
-:-
It's not until they're four planets into their adventure that he loses her. She's remarkably well-behaved, staying put when he tells her to and only running off if he explicitly says so, but he shouldn't really be surprised to misplace her.
It's Suffolk in August 1988; the weather is beautiful and Molly has just helped the Doctor fend off Reapers (she managed to ignore the part where he warned her several times do not touch eight-year-old you or you'll cause a rift in time, but it's fairly easily sorted) when a small boy with a mass of dark curls bumps into her. Immediately Molly apologises; the boy shoots her a disdainful look and darts off, while his older brother – tall; immaculately dressed, even for the beach; auburn hair – offers her an apologetic look. Molly gasps and her legs give out beneath her.
"Molly?" The Doctor asks, all concern, and she shakily stands and sprints back in the general direction of the TARDIS. He finds her behind the console, sobbing. He's never been good with crying women (Rose flashes into his mind and he shoves the thought away more viciously than usual) and opts to sit beside her, pulling her into an awkward one-armed hug. Eventually her sobs slow down enough for her to be able to gasp out, "Th- that was Sh-Sherlock. And John th-thinks he's d-dead now and in a week I've got to go to his funeral and God." The last word sets her off again, and it's a while before he can think of something suitable to reply with.
"There's a planet," he begins uncertainly, "Well, it's more of a moon really – anyway, its surface is essentially ice. Some nitroglycerin-based compound, I think. Regardless. The tribe that live there, they're called the Apeeshweh. They used to populate more of the galaxy, but there's only pockets of them left now. Nevertheless, they've got this tradition when a loved one dies. They pack the body in this ice stuff and publically mourn for twenty-seven days. And on the eve of the twenty-seventh day, they place the body on a raft and let it float out to sea. Then all the Apeeshweh who loved this fellow tribe member, they gather in a circle and discuss the deceased loved one – all their quirks, funny anecdotes, everything, right down from their smile to the times when someone would have quite happily murdered them. And after they've talked about it, they have this word – 'keshba'. It doesn't directly translate, but it essentially means 'life can be good again'. And they start living, more vicariously than they ever did before, because now they're living for this dead person that they all loved. They have something to live for."
She snuffles slightly, her mouth quirking up a tad. "What're you saying?"
"That even though Sherlock's gone, even though everyone's upset, life will be good again. That's a promise, Hooper."
She smiles and wipes her eyes. "Cheers. Being silly, s'all."
"What's life without silliness?" He asks, beaming like a four-year-old, and swings himself up. "Places, people, things to see, Molly Hooper of St Barts Morgue! Where to now?"
-:-
Ockenheim. Jotun. Fedelbard. The places blur together, the species and people become interchangeable, and both the Doctor and Molly know that all things must end.
-:-
He takes her to see the Quintle's sun implode. She nestles against him and says, "This has got to be the penultimate adventure, Doctor. I… I'm not cut out for this forever."
He knows it was coming, but it still feels like a stab in the gut.
-:-
He drops her back exactly four minutes after she left to get milk; no-one will have noticed her absence at all. They sit on the South Bank, legs dangling above the murky water of the Thames, sharing a bottle of Irn-Bru that Molly insisted on buying, and appreciate their final moments together.
"Life can be good here, Doctor," she says, swinging her legs. "I've got people who love me and besides, I can't stay forever. I've got a job. Responsibility."
"You've got to save the world," the Doctor corrects. She looks ready to argue but he smacks a hand across her mouth. "Not like that. Not with me. With your Sherlock and your Greg. Save John, save Stamford... maybe not the whole world. Just yours."
Molly smiles slightly, a sad curve of her mouth. "Thanks, Doctor." She kisses his cheek and takes his hand, squeezing it gently. "My door's always open if you want to drop by." She drops his hand and starts walking back towards the road, pausing and spinning round. "How long have I been gone?"
He laughs at the horror in her voice. "Six minutes." She beams and calls out a final, "Thank you!" before disappearing round the corner and out of her Doctor's life.
He'll miss her, because he misses them all, but she's not suited to this life forever. And of all the ways she would undoubtedly leave, this way hurts the least. He watches her go with a familiar fond ache and knows that for her, here, life can be good again.