The Doctor had become boring, locked away in that silly cloud. He needed to get out, have adventures. Give her a reason to create havoc.
Actually, there was a more urgent reason to it than just a relief from her utter boredom: the Great Intelligence could rise without The Doctor prepared. Worse: perhaps with The Doctor ready to give in! If that happened he could be erased from Time. Without his Ying, what good was her Yang?
It was no good leaving things up to chance.
She needed to go back into time and create something. Something that would be there at the right time to wake him, after the loss of those silly Ponds. Whatever he saw in that boring couple, she'd never know. Not to mention that horrendous offspring they'd created.
River Song indeed; a sassy swashbuckling Time Lady that stole the Doctors hearts? That was her job, thank you very much.
Now that they were gone, who was there to pull him up by his bow-tie? Yes, the Mistress. With the The Doctor married to the curly haired trollop the name took on a whole different meaning.
Soon she had traveled up and down The Doctor's timeline and it frustrated her no end to see how weak he could be at times. Why would losing one of those silly humans hurt him that bad? After all those years, had he still not learned that they could break at the slightest fall? She had tested that theory dozens of times whenever she was bored. But well, if he really needed an army of steel at his back and call, she'd soon fix that for him when her second gift was ready. She was certain he'd enjoy the surprise, but it would take a while yet to be finished. You couldn't build an afterlife in a day, could you?
So a division, a mystery to keep The Doctor occupied – and alive - till it was time.
She would gift wrap him a very special companion that would once more set him off on adventures.
A good one that would toughen him up a bit, made him strong.
She – it had to be a she, for some reason most men couldn't keep up with thew guy- she had to be strong, sassy and intelligent. She had to give back as good as she got.
If the Great Intelligence got to him, she had to have the brains to restore him. An impossible girl that would create a wonderfully messy mystery. Missy smirked when she thought about it. Oh, helping The Doctor was sometimes the same as confusing him, that was why it was so satisfying. If things went the way she hoped they would he could very well meet the same girl again and again. Well, if that didn't get his attention …
Even better: her perfect little companion would get a hold on him like no other: she would know every face, every adventure and more or less become a part of him. She'd think like a Timelord, well The Doctor. This was necessary, because there was trouble on the way. The Doctor was out of regenerations, and knowing the silly sausage he wouldn't think to ask for more. Well, a girl like the one she had in mind could fix that for him.
The new set of regenerations would make The Doctor boring. He'd be starting all over again and more or less be a baby Doctor, his memory shot, unsure of who he was. Useless. He needed a companion that would guide him – or kick his ass – the preferred option. The girl that knew every aspect of him would do the trick. This strong, glorious lass might even be able to BE the Doctor when the occasion called for it.
Now, where ever could she find such a perfect companion? This called for a lot of tampering and meddling with time. Missy's most treasured of all hobbies.
For a brief second she hesitated. Was she actually creating a woman to be The Doctor's savior? A play thing with no agency of her own life? Being a women herself now, she knew that would not do, that would not do at all. Of course not. Like herself, the Impossible Girl would be strong, independent and glorious: she'd have a mind of her own alright, she'd tell that silly man where to go, oh sometimes literally.
Cos she's perfect, innit? The control freak and the man who should never be controlled. You'd go to hell if she asked. And she would.
Her plan clear she set off to the autumn of 1981, where a very special leaf would fly into the face of a certain Dave Oswald to create events that would change the course of history.
Then she quickly dashed her Tardis to two decades and a bit later to lock a woman in a cupboard just to take over her shop for a few hours. Missy would have preferred killing her as she'd have made less noise, but she knew that would have led to too many questions afterwards.
There she was.
Missy smirked like a Cheshire cat: Clara Oswald, ready to receive the number of the best helpline in the universe.
Missy was certain it was all thanks to her:The dangerous combination of a passionate and powerful Time Lord and a young woman so very similar to him. She put them together and, with a well placed advert and certain less gentle actions involving getting rid of Danny Pink, who might have spoiled this perfect match, kept them together.
She was quite the matchmaker, she felt, and it was wonderful seeing them off on more exciting and more chaotic adventures. The Doctor became darker, more chaotic. Oh, she loved it.
Well at first.
Oh Missy, clever Missy. She did not see it all either, some things happen because of free will, because of the unexpected, because of feelings, because of love and friendship. Yes, she might have brought them together, and kept them together at certain points. But meddling alone could never create a bond as deep as the one The Doctor and Clara shared.
Never having known true love or friendship, besides what The Doctor tried to give her, this took Missy a long time to realise and even longer to understand.
And when she did, it hurt.
Slowly, over time something changed as deep down inside she grew to resent Clara as she watched her grow and change in The Doctor's presence.
Was she becoming too good? Had The Doctor become too reliant, too obsessed with the girl? Was she eclipsing her in his affections? How could this be? She was only a silly human, a puppy!
She decided to put her in her place.
Oh how Missy relished lording over her with that confession dial.
To wipe the smug smirk of that pretty little face. Pretty? Oh dear, a few moments alone in her presence and Clara had her wrapped around her little finger too. Was she starting to enjoy spending time with her? She feared she might be.
She had watched this girl grow up, had part in raising her. She felt warmth. Warmth she hadn't felt since her daughter …
That would not do at all, she had to snap out of it.
Tying Clara upside down a tree was a good start. Pushing her into Dalek sewers and into great danger was even better.
Turning her into a Dalek was perfection.
She had always known the girl wouldn't be killed, The Doctor was far too clever for that and she still needed Clara alive too. She just needed to be brought down a peg or two.
Just having fun at Cara's expense wasn't he only reason she'd put her inside the Dalek, it was a means to an end. It was urgent for Missy to make The Doctor see what was right in front of him, the one thing all three of them combined represented: The Hybrid.
“In a way, this is why I gave her to you in the first place. To make you see. The friend inside the enemy, the enemy inside the friend.”
Had The Doctor understood her there and then, it would have saved him a long timeout in a confession dial. But no, the man always had to take the long way round. And in the end had that interesting Me character hammer it home for him.
Back then he simply told her to run and she … walked.