The trouble starts after the happy ending.
Xoralia is a beautiful green world, inhabited by peaceful farmers whose technology is equivalent to early medieval Europe. The Xoralians would have no chance against aggressive, star-travelling warriors -- except that the TARDIS materialises in the tiny village of Skagada on the morning of the G'nadun invasion.
The invasion force is sent packing with a dazzling combination of technology, ingenuity, and agility. Jack, as decoy, leads the first landing party on a lively chase through the woods, where their heavy armour puts them at a disadvantage. One by one, they fall into the hidden pit-traps that the natives dig to catch the predators that stalk their cattle. The Doctor and Rose are "captured" while trying to sneak aboard the transport shuttle, and are promptly escorted up to the G'nadun star cruiser.
While the Doctor is being interrogated by the Task-Force Commander, Rose pulls herself up into the ventilation system, crawling through what feels like miles of duct-work before finding the right spot to leave the device that the Doctor hastily assembled. She retraces her path and drops from the ceiling into the Commander's office just as the Doctor is winding up his scathing remarks about moronic gorillas in space suits. She stands beside him, only slightly winded, a grin spreading across her dust-smudged face, while the Doctor announces that the G'nadun weapons systems have all been nullified. "You lot had better clear out an' head home quick as you can, before all the barracudas notice that the shark has lost his big sharp teeth." He turns to Rose, looking her up and down. "Time to go, Miss Rose Tyler. You need a shower."
The shuttle lands them out of sight of the village, by the edge of the woods. There they find Jack, leaning casually against a tree, whistling "We'll Meet Again". Together, they watch with satisfaction as the trapped G'nadun warriors are hauled out of pits by their jeering comrades and loaded onto the shuttle. By the time they walk back to the village, Jack's wrist-comp reports that the G'nadun ship is leaving Xoralian orbit.
Jack waggles his fingers in a vaguely skyward direction. "Goodbye!" he says in a syrupy-sweet falsetto.
"Good riddance," the Doctor growls.
"Good job!" Rose exults, and raises both hands so that she can high-five her two companions.
As soon as they convince the Xoralians that the invaders are truly gone, the trio slip into the TARDIS. It's the Doctor's intention to vanish promptly into the Vortex, but the TARDIS's erratic mechanisms nobble that plan. The gravitic anomalyser is acting up again. The Doctor and Jack crawl under the console, tools in hand. Rose heads for the shower.
Late the following morning, Rose walks into the control room, clean and well-rested. The Doctor, still beneath the console, is neither of those things. He sticks his head out just long enough to refuse a cup of tea, and to inform Rose that, if she is going to be so annoyingly cheerful, she can bloody well do it somewhere else. It is, Rose decides, a good time to go outside and get a bit of fresh air.
Less than ten minutes later, Jack joins her. He has been ejected for being "a ham-fisted idiot who doesn't know a spanner from a sparrow". Jack slips into a decent imitation of the Doctor's northern accent as he quotes this remark, his spirits unbruised by the slurs on his intelligence and technical competence. "When I left, he was muttering something that the TARDIS wouldn't translate," Jack reports, "but I'm pretty sure it wasn't love poetry."
Rose rolls her eyes. She's seen that mood before. "Let's go for a walk, explore a bit. He'll be feeling better by the time we get back."
"Rose Tyler! What d'ya think you were doin', you stupid little ape?"
"I don't see what's so wrong," Rose protests. "S'only a bunch of flowers."
"It was an offering, Rose -- a thank-offering. By accepting it from her, you might jus' as well have said, 'Pleased to meet ya, an' by the way, I'm a goddess.'"
"She was just a little girl! We saved her village, and she wanted to say thanks, and she picked some flowers. Little girls do that sort of thing."
"Yeah, an' that might have been all right, 'cept when her mum came around with a basket of fruit, Captain Charming jus' had to take one, and eat it right there in front of her."
Jack gives the Doctor his best "who, me?" smile. "It would've been rude not to. C'mon, Doc -- there was no way that I could've known that fruit was from a tree in the sacred garden of their shrine."
"An' then," the Doctor continues, as if Jack hasn't said a word, "you told her you'd bring the rest back to share with your friend. Now they think that we're all gods."
Jack grins. "I have been called divine more than once." The Doctor shoots him a look that would send a lesser man fleeing for his life.
"I still don't see where the harm is," Rose repeats. "We're only gonna be here for a few days, 'til you get the gravitic thingummy fixed, Doctor. An' besides, we are, sort of." At the sight of the Doctor's raised brow, she explains. "I mean, they don't even know about electricity. We're aliens with technology they can't understand, an' we saved their planet. Compared to them, we prob'ly do seem like gods."
Jack waits to hear what the Doctor's comeback will be. He knows what a Time Agency instructor would say to any cadet foolish enough to express that thought. The Doctor will be much gentler with Rose.
"S'pose you've got a point," the Doctor says mildly.
"Yeah. So, you gonna start worshippin' me?"
Jack blinks. There is not even a trace of a smile on the Time Lord's face.
Rose gawks. "What?"
"You gonna start worshippin' me?" he repeats. "Amazing alien, me. Saved your planet -- your species -- more times than you've had hot dinners. An' by my technological standards, you're both primitives -- yeah, even you, Captain." He leans back against the TARDIS console and crosses his arms. "Don't bother bringin' flowers." The tone is matter-of-fact, his face still unsmiling. He remains motionless as a granite statue, except for those cool blue eyes darting back and forth between his two companions.
Those eyes, Jack knows, can drill into you with the precision of surgical lasers. Right now, they are merely scanning the surface. Watching. Waiting. A voice in the back of his head whispers, What kind of god wears jeans and a leather jacket? And the same voice answers, A dangerous one. A sexy one. Jack imagines dropping to his knees in front of that dark, expressionless figure. A shiver runs through him, and he isn't sure if it's from fear or desire.
The tip of Rose's tongue flicks across her upper lip. "'S not funny, Doctor."
He keeps his gaze on her for ten interminable seconds. Rose seems to be holding her breath, and Jack resists an irrational urge to step between her and the Time Lord. The Doctor would never hurt Rose. Never.
"Didn't mean it t' be funny," the Doctor says. "I reckon the best time would be in the 14th century. Black Death all over Europe, Papacy bein' disputed, half a dozen new empires settin' up shop. Not much communication between continents. Makes it easier."
Rose seems speechless. Jack decides it's time to jump in. "Easier for what, Doctor?"
The Doctor gives him Annoying Smile #6: You're-not-usually-this-much-of-a-moron. "Easier to take over the Earth."
Jack's first impulse is to say, "You can't do that," but he bites it back, because he's pretty sure that the Doctor can do that if he wants to. The other Time Lords aren't around to stop him. The Time Agency might try, but they wouldn't have a chance.
The Doctor continues his monologue. "Cure diseases, startin' with the plague. Get rid of hunger. Stop the wars. You humans are such a violent species," he muses aloud. "Amazin' how many of each other you manage t' kill, even without advanced weapons."
Rose looks as though she's been hit over the head with a brick. "What about paradoxes? Reapers?"
The Doctor smiles approvingly at her. Good student. "Reapers can be avoided with a bit o' plannin' by someone who knows what he's about. Not a problem."
"Wrong? Savin' lives? Endin' misery? Isn't that what a god is s'posed to do?"
Jack finds himself itching to punch the smug SOB, even though he's figured out the Time Lord's game.
And so has Rose. Even before she speaks, he can see understanding, relief, and a hint of anger in her eyes. "Yeah. 'Cept it would take away their freedom. Turn them into puppets. An' you wouldn't do that." She smiles crookedly. "Y'know, Doctor, you can be a right bastard sometimes."
He smiles back at her, and the grim stone figure is once again living, breathing flesh. "S'pose I can be, yeah."
She hesitates. "Didn't mess things up too badly, did I?"
"Nah. This is jus' a tiny village, isolated. Rest of the planet won't even know that anythin' happened. Couple of centuries from now, some researcher will write a paper on myths of the Gada River Valley, an' put us in a footnote."
Jack adopts the dry tones of his least favourite lecturer at the Time Academy. "According to an ancient legend, the inhabitants of the Skagada region were saved from sky-dwelling demons by three supernatural visitors -- two handsome gods and a goddess with a charming smudge on her nose. This tale is clearly an allegory for-- hey!" Reflexively, he catches the bulbous yellow fruit that Rose chucks at his head.
"All right, you two," the Doctor chides. "Playtime's over. Captain, if you're ready to do something useful for a change..." He gestures at the open panel on the TARDIS console.
"So I'm not a ham-fisted idiot?"
"We'll see," the Time Lord grumbles.
Four hours and two cups of tea later, Rose returns to the control room, ready to explode with restlessness. "Doctor, I'm going outside. Need to stretch my legs for a bit, yeah?" She gives him her best smile. "I promise not to do any miracles."
The Doctor eyes her, then seems to decide that she can't get into too much trouble. "Don't go far."
"Jus' to the river." She wouldn't mind company, but she knows that the Doctor won't budge. Jack gives her a distracted smile before disappearing beneath the console. Right now, the only female that can hold their attention is the TARDIS. Blokes!
It's late morning, and most of the Skagadans are in the fields. The few who remain in the village bow respectfully when they see Rose emerge from the TARDIS, but don't approach her. When she reaches the river bank, no one is in sight. She finds a grassy spot just beneath a small ridge topped with sprawling bushes. At this point in its descent from the mountains, the Gada is only seven metres across, and it still skips and dances over a rock-strewn course, singing erratically to itself like a playful child.
The sounds of the river are soothing. Rose isn't sleepy, but she stares at nothing in particular, her thoughts drifting like leaves in the water. She thinks about the invasion; how well they worked together. They usually work well together, but lately it appears that they're getting even better. When did it change? Not all that long ago, Rose reckons. Five or six days ago, when she came back from that weekend in London. While she'd been at the hen party for Shireen's cousin, the blokes were on some space station in the 32nd century, shopping for spare parts for the TARDIS.
She noticed the difference first in Jack. He's quieter, Jack. No, that isn't exactly it. He still chats, jokes, laughs, tells outrageous stories about past adventures, but part of him seems to be somewhere else. When she asked, he said "I'm fine, nothing's wrong, don't worry."
Something happened while Rose was away, and she doesn't know all the answers yet. Jack's confessed to "a little run-in" with some Time Agents.
"I wasn't hurt. The Doctor wasn't hurt. We didn't even have to hurt the bad guys, okay? The Doctor talked tough, and then he did some jiggery-pokery with one of his gadgets, and we ran for the TARDIS. He might even have scared them enough to stop looking for me. So, stop worrying, Rose. Smile for me." And he had gently stroked the corner of her mouth with his thumb, encouraging it to curve upwards.
She had smiled -- always easy to smile at Jack -- but she hasn't stop wondering. There are other changes in him. He seems more… confident? No, that's silly. No one is as self-confident as Captain Jack Harkness. Happier, maybe. An' he's getting on better with the Doctor. Oh, they still snipe at each other, toss around insults, and challenge each other's skill and knowledge, but that's just a bloke thing.
There are changes in the Doctor, too. Harder to see, 'cos he keeps so much of himself hidden, but she can tell. He's more comfortable with Jack around. She knows he trusts Jack, has done for a couple of months, but something's different, so she'd tried asking him what happened.
"Y'should ask the Captain."
"He didn't have much to say."
"Not much to tell. Ran into a pair of Time Agents who recognised the Captain. They wanted to take 'im back to headquarters. Didn't want me."
"Prob'ly knew how much trouble you'd be. What happened?"
"I had a word, told 'em to leave our Jack alone, an' we ran for it. No fuss, no muss."
"Why do I think there's something you're not telling me, Doctor?"
"Rose Tyler." He said her name with a sigh, but his eyes were amused. "You're much too young to be so suspicious."
"I learnt from the best."
"Always the best, me. But there's nothin' to fret about. Nobody got even a scratch. We talked, I dazzled 'em with science, and we were off. End of story."
She'd felt reassured, but still perplexed. Something the Doctor said. It wasn't until she was falling asleep that the oddity struck her. Since when does the Doctor say "our Jack"? Rose had meant to ask about it in the morning, but that was the morning they landed on Xoralia. Now, on the sun-warmed grass, with the sing-song of the river in her ears, she has time to wonder about this puzzle.
Rose doesn't hear the oncoming footsteps until their owner is standing barely a metre away.