I started writing this in 2021, a direct follow-on to "Ma'at", but got distracted by real-life stuff and am making myself finish this now.
When I originally wrote most of this, Season 12 had aired but nothing more (i.e. before 'Flux'), so I made up an alternate Season 13, so to speak, with Graham and Ryan leaving as they did in 'Revolution of the Daleks' but an unspecified exit for Yaz, and Dan never got to travel as my OC Serene got there first.
Quick recap - Serene absorbed some of the Doctor's memories through a recall device implant on the day they met, then Missy 'gifted' some of her memories to Serene as well. The (Dhawan) Master later abducted Serene and damaged the implant, which is where we pick up:

The Doctor kept herself busy, so she wouldn't have time to think.
She checked in at the Exigency Station regularly, but Serene had been put into a medically induced coma and there wasn't anything she could do to help her best friend until she'd woken up.
So…

She went back to pick up the Metamorph Burrower, dismantling the machinery the Master had built.
What was left of it after the explosion, anyway. The containment field had held enough to stop the creature hatching, so the Doctor was able to retrieve it, and find somewhere safe to put it.
It gave her a little ethical quandary - it was a living being, after all, but its purpose was destructive, there was nowhere it could hatch that wouldn't eventually cause suffering. Even if she released it somewhere uninhabited, it would seed and spread to planets that were occupied.

The Doctor thought about storing it somewhere deep in the TARDIS, but there was always the chance it might somehow break containment, with all the travelling she did.
She could put it into the infinite Möbius trap within the TARDIS, like Serene had with the bloodhound the Ma'at cult had sent after her. But her friend having been able to access the trap not once but twice since made that risky too. That the Venandi creepers and Scyava shadow monsters within the trap hadn't eaten the bloodhound meant they might not actually be dangerous, but still, not a good combination.

In the end, knowing that she was kind of dodging responsibility, the Doctor delivered it to the Shadow Proclamation, who could keep it safely in stasis indefinitely.
If no-one else knew the Burrower was there, then it should be safe from those who might put it to evil purposes. And if the Proclamation decided to destroy it, then it wasn't her decision.
'Add that to the guilt pile…' she thought. 'So long as no-one ever tries to make you decide if there's balance in your life again, should be fine.'
It wasn't that easy to brush it off, but she'd done so before - and worse - and she had other things to worry about.

Finding the Master's TARDIS was easier now she had her own ship back. Deciding what to do with it was trickier.
Again, she could materialise her TARDIS around it, keep one within the other. But that could cause all sorts of physical and temporal problems in the long term, and her TARDIS really wouldn't like that. There weren't many people she'd trust with possession of a TARDIS, but there were so few time-ships left, and having sacrificed one to defeat the Daleks not so long ago, the Doctor couldn't bring herself to destroy or deactivate it either. Maybe she should take it to Gallifrey and leave it there…

But she still couldn't facing going back to what was left of her homeworld - and it was her homeworld, regardless of what may or may not have been her life before she remembered it - so the best thing to do was to hide it somewhere, locked and disguised.
Perhaps it was nostalgia, or perhaps because she knew that there were people there she trusted, if necessary, but in the end the Doctor went back to Earth and left the Master's TARDIS there. If it was ever needed, it could be found again.
"Something to be said for a functioning chameleon circuit," she muttered, walking away from the now-nondescript box. But she didn't say it loud enough that her own ship might hear.

The Doctor had been hoping something would come along to help keep her occupied, a good distress call to answer, something like that. She didn't dare try skipping ahead in time on the Exigency Station, in case she went too far and missed something important.
But she couldn't concentrate on exploring, couldn't lose herself in general travelling while she didn't know if her best friend was going to recover.

She thought about going back to the Ma'at cult, to make sure they'd imprisoned the Master, but she honestly didn't know what she'd do when she saw him again. This particular incarnation, she'd discovered, was very good at making her lose her temper.
'When I know Serene's going to be okay, then I'll go check up on him,' she told herself. 'He's my responsibility.'

In the end, she kicked about in the TARDIS for a few days, finally getting around to some basic maintenance, sorting through cupboards she hadn't so much as looked in for centuries. She rarely threw things away - who knew when something might come in handy?
And then she realised there were a couple of errands she could run. After the attempted uprising within the Zinariyan Alliance had been stopped, the Doctor had taken the belongings of Dr Tillin, an ally who'd been killed helping the Doctor escape, back to the woman's family, something she also rarely did.

Finding things past travelling companions had left behind… what best to do with them? She didn't want to put them on display, that would feel like she was building a shrine to those she'd lost. But she didn't like the idea of things lying around under beds and in the back of cupboards either.

So she started sorting. The bedrooms of those she might one day meet again, she didn't touch. Scattered items of clothing and accessories she tidied away in the wardrobe, books went into the library.
'Spring cleaning?' the Doctor thought to herself. 'Or is this me coming to terms with probably never seeing them again?'

While in the wardrobe, she set about picking herself out a new outfit. She'd already decided to keep the same coat and boots, but the blouse and high-waisted trousers weren't right for adventuring. A party, fine. Facing off against her enemies, not so much.
She wanted something like the trousers she'd worn for so long, but they were lost. And her clothes needed to be practical, so no skirts, dresses or heels. Nothing too flowing, or too tight. Jeans didn't feel right. A suit again?

Hmm. Other than the tux, nothing she had fitted properly, and she didn't want to go shopping. That reminded her… she'd bought some stuff at the Millefiori Galleria, the same place she'd started dying her hair pink.
The Doctor ferreted them out; a long-sleeved light jumper in emerald with a multi-coloured star motif, over a stripy t-shirt. Trousers… there was a bronze coloured pair she'd not seen before, and they fit. They weren't so tight that she couldn't move freely in them (she tested them thoroughly, running up and down TARDIS corridors to break them in, just to be sure).
And, of course, they had pockets.

She stared at her reflection in the mirror.
"Not too bad, Doctor."
She turned around to check everything fitted okay, wouldn't end up catching on things, or tangling up.
"Thanks very much, Doctor."
She grabbed her coat, slinging it on.
"You're welcome, Doctor. Are you sure about blue and green together?"
She stuck her feet back into her boots.
"My coat's more grey than blue, wouldn't you say? But if I get arrested by the Fashion Police, I won't say you didn't warn me."

Feeling much more like herself, the Doctor set about returning the things she'd found in the TARDIS to their owners. Those she knew where and when they were, anyway. River had taken away some of Amy and Rory's things, possibly to deliver back to her parents somehow, or to her other relatives, her human grandparents on 21st century Earth, perhaps.
As for River's own belongings… the Doctor thought about parcelling them up and sending them to somewhere and when she knew her wife would be, so that River's younger self could use them, but that risked tangling the timelines even more than they already were.

Those she'd parted on bad terms with, she decided to post them their things, or drop them off anonymously, unsure what reception she'd get. A few items she sent to the Black Archive or Torchwood, in case they proved problematic on Earth.
Those she didn't know where they were, she went to their families, (who of course had no idea who she was, in her current regeneration) and returned any belongings she thought they should have.
And then she tried to pull herself together, and went to visit old friends.

How better to distract herself from worry over a friend than by seeing someone else she cared about? It was difficult to do so with a new face, but it meant she could watch over some of them without them knowing who she was.
It was dangerous to get too close to Donna, but passing her by on the street in a different regeneration was probably okay? Just seeing that her friend was all right, that Donna and Shaun's kid was growing up okay, that they didn't need anything.
It hurt, of course, seeing her and not being able to talk to her friend, but it was better than nothing.

Graham and Ryan weren't home, when she dropped by, which didn't surprise her. She'd tried to keep in touch, when they'd first left, but Graham had quietly suggested she didn't visit for a while, to make it easier for them to settle back down.
Yaz had linked Ryan's vlog to the TARDIS so they could follow their Earth-bound friends' exploits, carrying on with saving the world, and being able to support people they knew at home at the same time. She hadn't been by in a long time, and after Yaz…
The Doctor pushed that thought firmly away.

The friendly neighbour told her that the two men were off abroad - no doubt saving the world again, the Doctor thought - and offered her a cuppa.
It was relaxing, sitting in a cosy front room in Sheffield, drinking tea and chatting about normal things. The Doctor found herself sharing her worries about her injured friend, and the kindly old lady was sympathetic and comforting.
Halfway through a packet of custard creams, a ringing noise emerged from the Doctor's coat pocket.
"Ah…just my phone. Excuse me."
The Doctor took out what was obviously not 21st century technology and examined it.
"What is it, love?" the neighbour asked.
"She's awake. My friend. I should go. Thanks for the tea."
"Oh, no problem. I enjoyed the company. I hope your friend's all right."
"Me too."

The Doctor hurried back to the TARDIS, then back to the Exigency Station.
By the time she got to Serene's room, her friend was sitting up, being examined. Professor Leyser was with her; it was she who had summoned the Doctor back, though by the look on the other woman's face, somewhat unwillingly.
The Doctor burst through the door, stopping in absolute horror at the blank look on Serene's face, no recognition at all. How bad was it?

Then a frown of confusion crossed her friend's face, as Serene chased a flash of memory.
"Doctor?"
"Yeah, it's me. Hi, Serene. How are you?"
Serene's face creased again, concentrating.
"I don't know. Everything is-"

She winced, reaching for the implant in her neck. The medic examining her intercepted her hand before she could reach the dressings covering the fused metal.
"I need you to be careful of this for a while. Eventually, surgical removal may be possible, but for now, try not to touch it."
"But I…"
Serene trailed off again.
"It should be helping me."

"We're here to help you," Professor Leyser said.
"Your memories may be confused for a while, but I'll do what I can to repair any damage."
Serene looked over at her, an instant smile of recognition rising.
"Do you have any lemon drops?"
"I do."

The Professor smiled back, reaching into her pocket and handed Serene a wrapped sweet.
There was a flare of what felt uncomfortably like jealousy in the Doctor's stomach.
'Not now,' she told herself. 'Serene needs help, you brought the Professor here to do that. You know they were friends. No time for jealous nonsense.'

The Doctor came further into the room, closing the door behind her.
"How long since you woke up?"
"Not long," the attending doctor replied, continuing to examine Serene.
"The brain wave patterns took a while to settle, but once they were close to normal, we began to bring her out of the coma."

"And do you remember..?" the Doctor didn't know how to finish that sentence.
"What happened? How you got hurt?"
Leyser threw an angry look at the Doctor, but her words were for Serene.
"There's no need for that yet. We'll begin a basic memory recall test once the doctors here clear you, and I've created a recovery programme for you. When they discharge you, we can go back to the Order and work from there."

"If that's what you want," the Doctor cut in, trying to be cheerful.
"We can go anywhere. Remember? All of time and space."
Leyser's expression hardened.
"This is not the time, Doctor. You asked me for help, and I'm giving it. You can't just whisk her away again, not this time."

The Doctor looked at her friend. Serene looked impossibly young just then, uncertain and bewildered, nothing like the woman she'd been. Had she lost that friend? Could she get her back?
"All I'm saying is, the choice is yours. When you feel better, I can… I'm here for you."
But Serene was still frowning, concentrating. She'd remembered Professor Leyser easily, but seemed unsure of the Doctor.

'The Professor's known her since she was a toddler,' the Doctor reminded herself. 'You've only known Serene a year or so. Don't expect too much.'
"Whatever you need," she continued.
"What she needs now is rest," the Exigency Station medic said, firmly. "And no excitement. You can come and visit tomorrow."

Chastened, the Doctor left, waiting outside. They didn't have tea in this galaxy, and the alternative was a strange, bright red tisane that smelled of wood bark. But it was better than nothing, and the Doctor had had worse, so she drank some while she waited.

After a while, Professor Leyser came out and sat beside her.
"I called you because I didn't know what she'd remember when she woke up, and she might have wanted to see you," the woman began, folding her arms, not looking at the Doctor.
"I know you care about her. But don't push her."
"I didn't mean to-"
"Honestly, I don't give a damn what you mean or don't mean," Leyser snapped. "Don't forget, you're the one who got her hurt."

Seeing old friends - or missing them - hadn't helped. It only reminded the Doctor of what she'd lost, and the recent going-over of her life in the Ma'at trial had already done that.
So she pushed all her anger down. She'd direct it where it belonged - toward the Master - when she knew Serene would be okay.

"I know. And I know you can help here, where I can't. But I can take her anywhere, any hospital, in any time. Whatever she needs. I brought you here because you know her."
"And if you hadn't erased all my work before, I'd be able to use it now to help her," Leyser reminded her. "It wasn't just your memories in my files."

"Alright, enough!"
The Doctor got to her feet, facing the other woman.
"Enough of the needling!"
Professor Leyser stared back at her, her own anger clear.

"You have no idea what people might do to get hold of information like that, do you?" the Doctor threw at her, trying not to shout, mindful that it was a hospital they were in.
"The contents of a Time Lord's memories? You think that attack by the Nevedi was bad? I've seen war like you could never imagine, and it isn't arrogance to say that there're a lot of people, monsters, creatures, that would destroy your whole Order to get at records of my memories."

"And yet, knowing that, you came to me for help," Leyser threw back. "Putting us all in danger, and you never even asked me what I'd do with my notes. I'd already locked them, and believe me, I wasn't going to start broadcasting my findings across the galaxy."
"I never thought you would. But you were safer without them."
"And you were the one to decide that? Without even consulting me?"
"This isn't my first rodeo. Sometimes, it's better for everyone if I just go, leaving no trace behind me."

"But you took Serene with you. Did she know how dangerous it would be, travelling with you?"
"I looked after her! We travelled for months with nothing bad happening; I didn't hurl her straight at my enemies. The Master… I never thought he'd take an interest in her, take her with him."
"He's your fellow Time Lord?"
The Doctor nodded, an intense weariness setting in. She sat back down.
"I almost always travel with a friend, and he knows that. He travels alone, and he forced her to go with him, mostly to hurt me, but also because he wanted to see what it was like, to have a friend. But he doesn't know the meaning of the word, and that's why he ended up hurting her."

Professor Leyser sighed, her anger fading.
"I know we must seem so tiny to you. But you have to understand-"
"You're not tiny. None of you are. I've lived a long time, and I've travelled far and wide. But I never see other people as tiny, just because they're not Time Lords."
"All right. We should work together, yes?"
"Absolutely? Shake on it?"
The Doctor offered her hand, and after a moment's hesitation, the other woman took it.
"This is for her, though. For Serene."
"For Serene."

The next morning, waiting once more outside Serene's room, the Doctor heard a familiar voice calling her name, and it took her a moment to place it. She looked up.
"Mabli? Is that you?"
Yes, it was the black-and-blue-haired medic from the ship Tsuranga in front of her, but she looked older now, dressed in the uniform of the station's senior medics.
"I never thought I'd see you here! Though now I think about it, it's not really -"
Mabli was cut off by the Doctor jumping to her feet and putting her arms around her.
"Oof. A surprise. Is everything okay?"
"I don't know. I brought a friend here for treatment-"
"And now you're waiting. I understand. Want to tell me about it?"

She sat the Doctor back down, and listened attentively as the Doctor told her all about Serene. How the recall device had absorbed some of the Doctor's memories on the day they met. That Missy had then 'gifted' Serene some of their own memories, before another incarnation of the Master had hurt Serene, damaging the implant and affecting her friend's mind.
"Okay. But it sounds promising, yes? She's in good hands."
"I know, I know. But… well, you must hear it all the time, how hard it is to sit and wait. Never been good at waiting, me. Now tell me about you! You look like you've been busy?"
"Well…"

Mabli tucked a strand of blue hair behind her ear.
"After you all left, there were a lot of enquiries. It took a while for them to believe any of what we told them."
"That's why I don't usually stick around for enquiries," the Doctor said, drily.
"Yeah, I can imagine. But eventually, they accepted most of it, reassigned me, and I just sort of… carried on. I put in my hours, I studied whenever I could, and, well… When you deal with what we had to, it sort of puts things into perspective. I realised I could handle a lot more than I thought I could, and after a while, my supervisors realised that too. I got promoted, and I kept on going, until I got posted here."
"Good for you! Glad they recognised your potential. I…"
The Doctor hesitated.

"Sometimes I wonder what I'd say to people, if I saw them again. What they'd say to me. I know it doesn't end well for a lot of people."
"I'm a medic," Mabli interrupted. "Things don't always go well for people I meet either. But most of them realise that things'd be worse without my help. As it was for us, when you came along."
The Doctor looked down.
"Not always."

"From what you told me," Mabli said. "This Master… he would've hurt anyone who was in his way, not just because she was your friend. I tell people not to blame themselves a lot in this job, because I know it fixes nothing."
"I know. I know. I just… I keep running into obstacles that tell me I should look at the damage I've done-"
"And whether or not it's worth carrying on?" Mabli said, astutely.
"You're not the first I've heard say that, either. Look around you, Doctor. This place specialises in emergencies and trauma. We face up to not being able to save all of our patients everyday, but we don't give up just because we can't save everyone."

The Doctor rubbed at her tired eyes.
"I know. This isn't the first time I've had these… doubts."
"Well, I'd be dead if it wasn't for you," Mabli replied. "As would the rest of the people on the Tsuranga. Losing Astos, and Eve Cicero, that weighed on me for a while. And I wondered how I'd cope with the next emergency, without someone like you there to help. So I figured out, I'd have to be the 'someone like you'. Not defeating monsters, as such, but knowing what to do. Being the one who can take charge and save lives. I expect a lot of people you save do the same."

The Doctor absorbed that quietly.
"Could've used a voice like you recently. Someone to shout out all the negatives."
"Well, that's probably why we ran into each other now," Mabli said. "The universe knew you needed someone to remind you of all the good you've done, and I get to say thank you for saving my life."
This time it was the medic who put her arms around the Doctor.
"Thank you, Doctor. And not just from me. From all the people I've saved, who might've died if I hadn't been there to save them. The ripple effect."

The beeper on her belt went off, and Mabli got to her feet.
"And there's another one now. I hope your friend gets better."
"Thank you, Mabli. Best of luck with… you know, everything."
The medic gave her a smile, and dashed off toward the next emergency. The Doctor continued to wait.

After a little while longer, when Serene had been examined once more, and Professor Leyser had performed a few basic recall tests, the Doctor was allowed in to sit with her.

Serene seemed more like herself, but she was still confused. The Doctor brought the multi-coloured wrap Serene had bought in the Millefiori Galleria, to put over her bed, hoping it might spark some memories, and they spent a few hours just talking.
The problem, it seemed, wasn't so much memory loss as it was that the trauma Serene's brain had undergone had left her confused as to what was reality and what was fiction, mythology, or other things she had learned through reading, rather than experience. So the Doctor slowly went over their travels together, sorting through what they had done and seen.

Over several days, her visits spread out so as not to tire Serene too much, the Doctor began to realise there was another problem, namely that some of her own memories had remained in Serene's head, as did some of Missy's.
While that wasn't necessarily a problem, it meant that Serene was struggling to tell which things she had actually done, and what she thought she had but was in fact a Time Lord memory.

'And if a person is the sum of their memories, then what happens when their head gets filled up with someone else's?' the Doctor worried.
And she was right to be worried. There were moments when Serene was nothing like herself, when she struggled to even know herself, confused and frustrated.
And worse, when she brought up a memory of Missy's, it was like she was reliving the experience and she changed in front of the Doctor's eyes, taking on Missy's mannerisms and speech patterns.

She sometimes did the same for the Doctor's memories, which was exceptionally weird for the Doctor, but they had taken care, before, to remove anything traumatic or potentially damaging from Serene's mind, (not to mention anything too private) so the memories were less vivid. Serene sometimes had nightmares about facing monsters and enemies she had, in reality, never even met, but she seemed to accept that they weren't her own memories, having less impact.

Could they remove Missy's memories, now the recall device was destroyed? It had made separating out the Doctor's memories from Serene's easier, but even with Professor Leyser's expertise and Serene's connection with the TARDIS, this was going to be tough.

Once Serene was discharged from the care of the Exigency Station, the Doctor took her and the Professor back to the Cerebral Order.
Being in the TARDIS seemed to help a little, and they let Serene wander the corridors for a while, spend a little time in her room. The Doctor kept her out of the room that displayed the Doctor's own memories, for the time being, worried it'd be too confusing.

And then they started work, in Professor Leyser's lab. It was similar to what the Professor had done for the Doctor, when her own memories had been mis-firing around her brain, and it took a while. Every now and then the Doctor, knowing her friend was in safe hands, couldn't control her itchy feet any more and nipped off in the TARDIS for a few quick trips.

Eventually, Serene seemed recovered. She had control over her recall, didn't lapse into anyone else's mannerisms and appeared almost her own self again. She could be hesitant still, at times, but she and the Doctor worked out how to deal with any problems, going forward, and soon they were both keen to be off.

Serene had enjoyed the calm of the Order for a while, walking in the gardens, but as she came back to herself, she remembered why she'd wanted to leave in the first place, and became excited at the thought of travel again.

A little reluctantly, Professor Leyser let her go, with the proviso that they come back immediately if there were any future problems. The Doctor offered to take her along too, and she could see Leyser was a little tempted, but she decided to stay and go back to her usual work. This time, the Doctor let her keep her notes.

"Anywhere in particular you want to go?" The Doctor asked, closing the doors and starting dematerialisation.
"Somewhere old, somewhere new?"
Serene thought about it.
"New. Going back to places we've already been seems like a waste of time. If there's anywhere in particular I've forgotten that you want to remind me of, than we can do that, but…"
"Onwards and upwards!" The Doctor grinned.

They travelled for weeks, gently, and almost without incident. Mostly, Serene's hesitance had gone but occasionally the Doctor would catch her just staring blankly into space, as if she was still glitching, and sometimes she'd say odd things, mentioning places she'd never been, people she'd never met.
The Doctor found the best way to tell her she wasn't being herself was just to say her name. As a child, other members of the Order had used her name to remind her that she should be calm, still, sedate or just to behave. Now the Doctor found she was using it to bring her friend back to who she was, the person she'd discovered herself to be through travelling.

Eventually, Serene started to demonstrate a kind of restlessness.
"What is it?" the Doctor asked, glancing up from the console to where her friend was pacing.
"I need to do something," Serene replied, not stopping or looking at the Doctor.
"I don't know what, exactly, but I just feel this need… we need to fix something."
"Fix something?" the Doctor repeated, frowning.

There was a tenseness to Serene's posture.
"Yes. Find something broken and fix it. Put things right."
The Doctor's frown slipped to a smile.
"Not gonna argue with that. Something big, or shall we start little and work our way up?"

But Serene didn't stop pacing.
"I just… it's like I can feel all the bad things in the universe. We've been travelling for fun, but there's so much out there, so much good we could do…"
The Doctor left the console and intercepted her, putting a hand on her friend's arm.
"Hey. It's me you're talking to. This is what we do, yeah? It's been fun because I didn't want to throw you into something you weren't ready for, and cos I don't want to risk you getting hurt again. But I'm not gonna wrap you in cotton wool. If you want to go topple a few empires, or throws spanners in the works of some evil plans, then I'm all for it."

Serene didn't reply for a moment. Then her expression cleared, and she smiled.
"Good. I'm ready."
The Doctor opened up the universal frequency for distress calls, and off they went.