My idea was that, throughout season 5, the Daleks would almost appear, but be busy elsewhere. The second-to-last story of the season, which I hadn't thought up a plot to, yet, would vaguely involve the Daleks, but show that they really are busy somewhere else.
The Doctor, Jenny, and Seo would decide that whatever plan the Daleks were up to, they needed to find the Daleks and stop them.
Then — right in front of Jenny and Seo's eyes — the Doctor disappears into thin air. For no apparent reason.
That'd lead into my season finale.
Season 5 Finale
At the end of the previous story, the Doctor disappears. He is whisked through time and space using surprisingly sophisticated technology; he remarks on this when he arrives.
When he does arrive, the Doctor blinks. Stares at the area around him.
The place is completely wrecked, like someone's gone through and smashed everything up, or started a war in there, or something. But it's been patched up, since, and the technology that's been patched is absolutely brilliant.
Some of the technology, the Doctor realizes, is incredibly close to Time Lord tech.
"Welcome, Doctor," says a voice from the shadows. There's a sound of a machine drifting into view.
It's Davros.
"Davros," the Doctor sighs. "Of course it would be. How did you escape, after that business with the reality bomb?"
Davros laughs. "I had… help."
"Help?"
Davros presses a button, and two tanks of green goop light up behind him. The tanks contain two comatose bodies, lying inside.
Seo and Jenny.
"Such dutiful children, Doctor," says Davros. "They watched you disappear. Didn't know where to find you. They traced you to the Crucible, ran into the flames to drag you out. But you had already left."
"And they found you, instead," the Doctor realizes. He curses within his head. "How did you convince them that you were me?"
"With… difficulty," Davros replies. "At first, they didn't know the difference. They thought you'd been badly burned by the flames. When they worked it out… I 'persuaded' them. With a few small surgical procedures."
The Doctor gets very angry at this.
"Tell me what happened, Davros," says the Doctor. "Tell me everything!"
Here's what happened:
After the Doctor disappeared, Jenny and Seo raced off to the TARDIS, to get it to find him. They managed, with a lot of fiddling around, to work out how to fly it. Then they tried to follow any trace they could of the Doctor.
But they knew he'd been transported elsewhere in time and space using a technology they'd never seen before. So they couldn't trace it.
Then they get an inspired idea.
They can't trace what took the Doctor, but maybe they can trace him. They reason that if a stabilized exploding star, held in the second just before it collapses, can create a web of time, that they should be able to use a similar trick to map a timeline for one particular person.
("They destroyed a star?!" the Doctor shouts.
"Oh, no," Davros replies. "I believe they tried to destroy your TARDIS."
The Doctor freaks at this. Apparently, Jenny and Seo didn't realize that blowing up a TARDIS could potentially unwrite the universe. Good thing they avoided that!)
Actually, what they do is very clever.
They notice that the TARDIS, upon self-destructing, will loop the inside time continuum, to stop the calamity. They rig that feature up so it acts as a full-scale time reversal feed — which they can do by fueling it with power from the explosion that won't happen, creating a paradox that'll vault them even further away from the incident.
The TARDIS is linked to the Doctor; therefore, capturing it in a specific way in a specific location in the universe will allow them to view his time stream at that point — like a map.
They did this to find out where and when he was. They gathered that he'd been whisked away to the Medusa Cascade, and they sent the TARDIS off to that spot.
.
"They tracked down the wrong me," the Doctor says.
"Yes," Davros agrees. "Amidst all that chaos and time, nearly blowing up and destroying the universe… you can't blame your TARDIS for being a little… confused."
No, of course not.
Only natural.
"They thought that you'd been kidnapped by the Daleks," Davros says. "They never thought that, by saving someone from certain death… they'd be dooming you to die."
.
We cut to the past, where Jenny and Seo land the TARDIS on the crucible, shortly after the 10th Doctor's TARDIS has dematerialized. Davros is being consumed by the flames, his face and flesh scorched beyond recognition.
Jenny and Seo emerge from the TARDIS, and run through the flames.
"There! I see someone!" Jenny cries, extinguishing the flames around Davros.
"He's hurt!" Seo says, checking him over. "Jenny, he doesn't have any regenerations left! If he dies… that's it!"
They take Davros back into the TARDIS, and launch it, getting away from the flames. The TARDIS, however, senses that Davros is inside, and does a nosedive. It crash-lands into a nearby planet, very violently.
Seo and Jenny try their hardest to revive Davros, still thinking he's the Doctor, but they're losing him quickly.
"Who knows how long the Daleks had him, before we arrived!" Jenny says. "I think they did something to him." She shows Seo a scan she ran.
"They tried to turn him into a Dalek," Seo realizes, understanding the scan. She points at his chest. "His whole chest is just… a mess! Like someone peeled away the skin and most of the organs!"
It's such a mess that they can't tell that Davros has only one heart.
They do, however, figure out how to create another life-support chair for Davros. They figure that by adapting Dalek technology and melding it with Time Lord technology, they can reverse what the Daleks did and make the Doctor himself, again.
Thus, they created a life-support chair with substantial regenerative abilities.
.
"And when you'd regenerated enough," the Doctor guessed, "they began to realize their mistake. So you had to 'persuade' them."
"Yes," says Davros.
.
Cut to the past, where we see Davros operating on Jenny and Seo, by cutting into their brains. They are screaming on an operating table, but restrained.
.
"When they recovered from the operation, they became good little girls, again," Davros continues. He gestures around himself. "They were extremely helpful. I couldn't have done any of this without them."
"Let me guess," the Doctor says. "Daleks with horns!" Before Davros can speak, the Doctor cuts in, "No, no! I got it! Dyslexic Daleks, that call themselves Dakels! Or… oh, don't tell me you made Daleks out of chocolate? That'd be brilliant!"
"I did not make Daleks!"
The Doctor laughs, hysterically. "Oh, come off it, Davros! You always make Daleks! You might call them something a bit different… but in the end, they've all got the same bumps."
Davros fumes.
"I admit, I did seek out the Daleks, at first," says Davros. "But they were weak. They were corrupted! They were…!"
The Doctor laughs even harder. "The Daleks from the progeniture machine!" he realizes. "They rejected you! Just the same way they rejected the Daleks you made from your own cells."
"I did not need them, anymore," Davros replies. "I took control of your TARDIS. And found this place. Its species a primitive and miserable bunch. With the help of these two lovely children, I turned that species into something… better."
The Doctor's laughter dries up. "What have you done?"
.
Davros created both a race and an entire society, with help from Jenny and Seo. He convinced them that they were helping the native life forms on the planet, creating a technology that could help them ward off the Dalek aggressors who were soon to return.
Davros soon discovered that Seo and Jenny may be very smart individually. But together, they're absolutely astonishing. More brilliant than anyone.
("Even me, Doctor," says Davros. "Even you.")
When Seo and Jenny started creating amazing things, Davros operated on them a second time, to boost their combined intellectual capacity.
Seo and Jenny constructed an entire civilization, full of technological marvels that not even the Doctor had seen before, in only a few months.
.
"But that level of mental activity would burn them out!" the Doctor snaps. "They'll die."
"Yes," says Davros. "After a year. But there's always another regeneration. Another year. And another. And another."
The Doctor grows even angrier. "I won't let you murder them, Davros!"
Davros continues with the story.
.
Seo and Jenny were thinking so hard, they started to pass out. In desperation, they'd shut part of their minds down, to stop themselves from burning out.
That's when they finally saw past Davros' deceptions.
They realized that they were torturing innocent creatures and turning them into monsters. Then building horrible technology for a man who definitely wasn't the Doctor.
"Don't let on that we know," Jenny says. "We play along. But, when he's not looking…"
"…we turn the whole operation against him," Seo agrees. "Then fight back, when we know we can win."
.
Now…
"Judging by the state of the place," the Doctor comments, looking around himself, "they almost succeeded."
"Almost," Davros agrees.
.
When Davros overpowered them, he knocked them out cold.
He then placed them both in a kind of telepathic, aerated green water, in which they wouldn't be able to stop Davros' mental conditioning or prevent the exchange of ideas. There, they remain — still bouncing ideas off one another, still brilliant, still helping to create a new race for Davros — but unable to escape.
The telepathic water is used to control and influence their thoughts, too — although, as Davros points out, this isn't hard. No matter what's on the surface, deep down inside, they are the Weapon and the Soldier. Both are created for war and death — it's the core of who they are.
.
"They were the ones who brought you here," Davros finishes. "A teleport able to break right into the TARDIS and pluck you out. Leaving no trace."
Thus, Davros finishes his gloat, and finishes his story.
.
The Doctor escapes Davros, before Davros can kill him. Then he runs.
"But you two aren't just going to give in, now that I'm around," the Doctor knows, thinking back to Seo and Jenny. "Even if he's changed around your minds… you'll know the truth, now. You'll be able to resist."
And, yes, he's right!
Seo and Jenny are fighting back more than Davros thinks. And have been for some time!
The Doctor discovers this when he realizes that Seo and Jenny have built in a self-destruct function into all the technology, built around a central hub point. And the code to that central hub point is a number that the Doctor knows from their travels together.
The Doctor topples Davros' war machine and frees Jenny and Seo.
Just when the Doctor thinks everything is all resolved and settled, the Daleks attack. Turns out, they had some angle on this operation as well, and have been manipulating things for their own personal gain. There is a plot twist in here, and everything gets turned on its head before the Doctor et all can figure it out. Probably, they will wind up having to deal with the Daleks by using Davros, who has been manipulated.
Anyways.
In the end, it's Jenny who wipes out Davros' new race. She knows that they will rise up and terrorize the universe, and that she, as their creator, has a duty to destroy them. Seo tries to stop her, claiming it's genocide and they have to change these people and teach them better ways, but it's too late.
The Doctor finds out, and is furious at them for committing genocide. He assumes it's Jenny behind it, and mutters about her still being just a soldier at heart. But when he checks the evidence on hand, he discovers that it's Seo.
Turns out, Seo has rigged the evidence to prove that she was the one who did the deed, and Jenny had nothing to do with it.
Jenny asks Seo why she did it.
Seo explains that "Even if Father hates me, I've got a mom who loves me and will understand." She gestures at Jenny. "You've only got him."
The Doctor drops Seo off with her mom, at the end of this. He mentions that if she's committing genocide, she can't travel with him anymore — and her mom will punish her severely for this.
After Seo leaves, the Doctor drops off Jenny somewhere else. He mentions to Jenny that he's pretty sure Jenny was the one responsible for the genocide, and Seo took the blame, but he can't prove it.
He tells Jenny, just before he leaves, that she should remember this forever more:
"She's more human than you," the Doctor says. "And that means she'll always be more prone to mistakes, to violent outbursts, to passions of love and rage, to acting stupid even when she knows it's stupid… and perhaps even means she'll never be quite as clever and sneaky as you are, Jenny." He looks into her eyes. "But it's her humanity that will save you, Jenny. It's saved you now, and it'll save you again. Every time."