Trying not to steal too many plot points from 'The Immortal Janto Series', but all my ideas pale in comparison XD I'll try my best though

"I guess that means its worked" John groaned as he picked himself up off the floor; only the Doctor had been prepared for the sudden movement and the other two men had ended up piled rather unceremoniously on the grated floor of the time machine. They'd barely managed to righten themselves when a second bout of turbulence had them flailing for the nearest purchase.
Ianto's gun had fallen from his hand, abandoned in favour of the railing which he was now gripping onto for dear life. The Doctor picked it up, holding it away from him like it was some deadly animal which might attack him if it got too close.
"Where did you get this?" he asked the Welshman, placing the offending item rather gingerly into his pocket.
"There's a lot of rooms in here..." Ianto shrugged, looking a little guilty: he knew how much the Time Lord hated firearms.
"Yeah nice ship you've got, handlings a little wobbly and the interior decorating would drive anyone with OCD mad: but anything's an improvement on the sewer chic" John was slowly regaining his confidence back- especially now Ianto was unarmed. He grinned a little when he caught the younger man's eye roll, whatever had changed about the Torchwood employee it hadn't effected the best of his idiosyncrasies.
The fake Captain was a little nervous about seeing Jack, and a little angry that after all the speal the immortal had given him about how beautiful and awe-inspiring the Earth was he'd left himself only a year or so later.
It seemed all three men had a lot they wanted to talk to Jack about, some subjects less friendly than others.
With a final echoing roar the TARDIS engines settled and the occupants were able to release their hold on the railings, no one was particularly eager to step out first: not knowing what would greet them, but they could establish that Jack could be nowhere near by, as he'd have come running at the rather unmistakable sound of the TARDIS materialising.
The Doctor- more accustomed than the others than stepping into the unknown- went first, closely followed by Ianto and a slightly reluctant John. What greeted them was a plain of sand dunes, spotted with what could have been Marram grass, slopping down to the sea. Of to their right was a towering citadel of grey stone.
"Looks like the poster boy came home" John observed: he'd recognise the Boeshane Peninsula anywhere; it had been infamous for most of the 51st century after the Alien attack he later learnt had torn Jack's family apart. It hadn't been the first attack on a human colony in the area, but it was by far the most brutal. It had taken centuries to reclaim the area and the population remained low for many more: no one really wanted to live on the sight of such a massacre. But the most important thing John noted about this particular city was that it was where the Time Agency later set up an outpost.
No one spoke as they entered the city; they were well aware of the stares they were attracting: sporting such bright, diverse clothing. This place reminded Ianto of one of those recreation towns, where everyone dressed up like they were from Victorian times, but if you looked hard enough you could see people wearing modern watches, or jewellery, or perhaps a car hadn't been hidden properly.
This place really was strange: everything- while futuristic and high tech- looked old, ancient almost; the two extremes.
"What do you suggest we do?" Ianto asked as the reached what appeared to function as a town square. "Just wander around until we find him?"
"With any luck he'll see us..." the Doctor hadn't given much thought to this end of their hunt: the chance of finding a signal had been so remote that even with his boundless positivity he'd half expected it to fail, and therefore hadn't planned this far ahead.
However it seemed fate (or at least a twisted incarnation of it) was on their side and it took mere moments of aimless wandering before the Doctor caught a glimpse of strikingly familiar coat tails disappearing around a corner.
He took off with little warning to the others, Ianto quickly caught up with him however, more than used to people who started running after things without explanation.
They found themselves in a network alleyway, away from the crowds, they were still catching no more than glimpses of the person ahead as they rounded corners, but eventually they got close enough and the Doctor was able to call out to the person.
They caught up as the person halted, on closer observation they could tell without their target even turning that this wasn't Jack.
John was not prepared however for who it really was; it had been a while since he'd seen a fellow time agent other than Jack.
"Scarlett?" he exclaimed, the person they'd been perusing was a young looking woman with long raven hair, tied up in a ponytail and tucked into the back of the long coat which Ianto was almost certainly sure was Jacks. "What are you doing here?"
"I could ask you the same question" the woman sounded just as surprised as he was, her accent was strong, the nearest likeness Ianto could think of was south American. He also noticed the wrist-strap on her arm: similar to Jack and Johns but more streamlined.
"We're here looking for Jack" the Doctor spoke up, he wasn't sure quite what to think of this woman yet, the other times agents he'd met had a history of being unpredictable and he wasn't going to take any chances with this one.
"Why? What do you want from him?" she snapped, John was slightly taken aback by her sudden anger: she'd been close to Jack- they all had- but never enough to be so protective over him.
"We're just old friends" the Doctor tried to reassure her, throwing in a smile for good measure.
She narrowed her eyes slightly but seemed to accept their answer, gesturing for them to follow her.
"He will not be happy if you have lied. He asked not to be disturbed" she seemed to be solely addressing John as he fell into step beside her, leaving the others to trail behind.
"What about you? Last I heard you were on the other side of the universe, new frontier and all that"
"The time agency wasn't the only thing that fell" it was the only answer she gave, and John knew better than to push her: like Jack and himself all Time Agents had their own very diverse set of skills and, more often than not, a matching set of psychological problems.
After winding through the maze of alleys for a bit longer- Ianto and the Doctor growing increasingly more anxious: they didn't know this woman but their experience with ex-time agents wasn't exactly comforting- they reached a rather imposing looking door, solid iron tinged with rust and locked with a huge bolt which slid back when Scarlett held her wrist-strap up to it and tapped out a series of buttons.
The inside of the building was very scarcely furnished; just a few chairs and a table covered in an array of futuristic technology- only some of it resembling the retro style of this planet, the rest probably came from elsewhere (both time and place) and the Doctor couldn't help feeling uneasy about its presence here.
There was only one door leading off the room and no windows, just a single bare bulb dangling from the cracked ceiling.
"Why are you here?" John asked again, picking up one of the devices on the table and examining it.
"The Time Agency took something from both of us. I for one would like it back"
"Your thing is easy enough: its tangible, but his memory?" John scoffed, setting the item down "Is he still deluded enough to think that's possible?"
"But it is." Scarlett insisted,
any further discussion was cut off by the door across the room opening and none other than Jack Harkness entered the room.
He froze as he saw Ianto, face twisting in a flood of emotions then quickly going blank; he took a few steps forward, eyes flicking from Ianto to the Doctor.
"It's really him Jack." the Doctor insisted, aware of what was probably going through the man's mind.
There was a moments silence as everyone waited for Jacks reaction.
"No."
No one was more surprised by this than Ianto; he stepped closer, hoping to comfort the immortal. "Jack..."
Before anyone could react Jack had drawn a gun, the Webbly revolver that Ianto had seen him use to take down so many threats in the past, and pointed it straight at Ianto's head.
"It's not you. It can't be" he said through gritted teeth, hand shaking a little.
"Jack, it is me. I promise." Ianto took another step forward, tears starting to well up behind his eyes.
Nobody was prepared for what happened next: Jack pulled the trigger and Ianto's lifeless body fell to the floor.

I feel so evil... Late update and clffhanger XD Though I can't take all the credit: thanks to 21stCenturyGirl for the idea! This time it was Tony to the rescue XD