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The TARDIS is not a place that really needs to be cleaned.
Why would it? It’s a trans-dimensional entity that can pick up and drop off rooms whenever it wants, adjusting to the directions of the Time Lord that drives it.
(Or, in this specific case, the needs of the Time Lord that ran off with it, the Time Lord that the TARDIS claimed as its own, the Time Lord that sometimes is too soft and too hollow and too broken down, sobbing against the grates or digging their nails into the console or pacing the floor after yet another companion leaves or gets left behind or dies.)
When companions come on, the rooms are temporary things that spring into being in response to each one’s wishes and likes and preferences. Sarah Jane got a desk with a typewriter (and eventually a tablet, when she hit a century that introduced her to that particular technological invention). Captain Jack got a room tricked out with the latest of tech embedded in the walls, including a holographic projection of Boeshane, and yet a rather spartan layout when it came to the bed and the furniture, nothing more than a bed and a wardrobe. Vislor Turlough got a room that mimiced rooms back on his home planet, albeit with any possible weapon removed because the TARDIS was not willing to let her Time Lord be murdered because of something that she had provided.
Rose Tyler’s room had been pink and yellow, filled with laundry that was tossed behind after she took off running and trinkets she collected from various planets and the remnants of the nineteen-year-old girl with enough reckless bravery to restart the universe.
Every companion’s room disappeared the moment that they left the TARDIS, save Rose’s.
The Doctor has been keeping it around as a sort of memorial. A ghost of a girl that had radically knocked his life off of its path, reminding him of the worth of cowardice and kindness, and then drove them both down the path towards their own destruction as they made each other more self-destructive than ever.
The TARDIS went to erase it after Donna got into the TARDIS, at the possibility of a new companion, but it didn’t work out, because the Doctor clung with bitter, aching, bleeding fingertips to that room. To the life that had once lived in it, no matter how impossible it would be for Rose to return.
But then came Dr. Martha Jones.
It is impossible to ignore the way that Rose Tyler existed as a ghost throughout their entire relationship, the echo of a girl that was gone but not dead, too much to be left behind, too much to continue.
It’s not as if the TARDIS doesn’t see how Martha Jones glows in her own way. The way that she pushes the Doctor just as much as Rose did, the way that the Doctor opens up to Martha even in a way that he never opened up with Rose, because Martha knows how to poke and prod and peel, because Rose was bright, Rose was a supernova in progress, but Martha Jones is a doctor.
There have been so many companions that flare and fade, that burn brighter than a Time Lord could ever handle, because it’s a reminder that one day they will be ghosts. There are companions that become Bad Wolf, that save him from Time Lords, that are destined to become hybrids and DoctorDonnas and the Bang Bang itself-
But Martha Jones is the woman who walks the earth. The woman who has to deal with the Doctor when he is grieving and making no effort to hide that fact, the Doctor when he is made of shrapnel and ache and not enough patience and not enough kindness. The Doctor who is rude and callous and yet-
Martha falls in love with him, and there is some part of the TARDIS that recognizes that he is attracted to her, in return. The part of him that kissed her when he could have imparted his DNA in another way. The part of him that is wounded and aching and cruel, because he has lost everyone and everything and Martha is the person who looks at him, who sees him, and yet wants to know more.
Martha leaves, eventually, as she always would have, because she sees the fact that right now, he values his own grief and his own heartache over hers.
And it is only in the moment that she leaves, the moment that the door swings shut behind her, because she finally chooses herself, that Rose Tyler’s bedroom finally disappears. That the TARDIS watches the Doctor finally accept the fact that Rose Tyler isn’t coming back. That he fucked up the person who was willing to put up with him at his worst, under the Chameleon Arch, in 1969, in the fact that he watched her family be wrecked for a year straight and yet still grieved the man who hurt them more than he grieved their sorrow.
Martha Jones got out, and it was only her finally getting out, her finally being too burned by too many ghosts, that makes the Doctor start to understand the fact that a companion is not just your companion in the good times, not just a companion to watch you sparkle or to help your star burn, but rather, a person unto themselves.
A person who the Doctor witnessed the beauty and glory of, but couldn’t see properly. Couldn’t appreciate it properly.
Millenia ago, a Time Lord stumbled into the TARDIS’ home and ran away with her, and he has had so many companions since. He has watched so many people live and die and burn bright as stars until they all go supernova and he is left living the life of a nebula, birthing himself again and becoming a new person and never having to live with his decisions in the moment in the way that a human has to.
So many of his companions go the same way, burning themselves out at the altar, burning themselves out until they go supernova as well or he leaves them behind they can burn themselves out in front of him. The Adrics, the Roses, the Jacks- he can’t bear to repeat them.
Martha Jones is different. She got herself out. She decided to stop the cycle.
And yet, in those last moments- she hugged him, because she saw that he was burning himself to the ground, too. She saw that he would soon become a ghost if he didn’t stop himself.
And the doctor has had so many companions over the years, so many bright stars and brighter suns, but Martha Jones is the closest to him, whether he likes to admit it or not.
Even with all the Time Lords and half-immortals and aliens that travel with him, Martha Jones is a doctor.
And in this past year, with the Doctor incapacitated, with the entire world collapsing and burning around her, she became the Doctor.
Rose Tyler’s room disappears, but Martha Jones’ room remains. Not because the Doctor asks the TARDIS to, but because in those long, long months trapped in 1916, the TARDIS got to spend more time alone with Martha Jones than any other companion since maybe even Susan herself, all of those centuries ago.
The Doctor might think that Martha Jones is a chapter with an abrupt ending, might just be waking up to the idea that he cared about her more than he ever let himself admit, but the TARDIS knows that Martha Jones will be back, some day. Whether for one adventure or many.
And when she comes back, the TARDIS knows that the Doctor will be a bit more ready to finally speak to Martha as who she is, not a replacement for a ghost, not a girl who burned herself out for a crush, but a woman who refused to go supernova because she respected herself, because she wanted to stay home and help the people she loves heal.
More a doctor than the Doctor himself could ever be.