This idea is probably way cliché, but. Spoilers for New Who Season 3 finale, PG-13/T for swearing and some non-graphic violence.
He's good at hiding and he's good at running but he's not that good, and it's barely two months before they find him. He doesn't know what's happened to the others, to Gwen and Tosh and Owen, but he hopes they have better luck than he does.
When they capture him they do it quickly and cleanly and he wakes up in a cell. They feed him well and he eats better than he's eaten since . . . since, and they don't touch him, don't hit him or hurt him or bind him or even talk to him. After a week he's allowed to wash and given a clean suit, identical to one in his closet back home. Maybe it's the same one; it wouldn't surprise him.
He's led to another room, down long winding corridors of pipe and wire and if he had to guess he's probably on a ship of some kind, maybe even the Valiant. And when they arrive at the engine room he knows who's going to be there.
Harold Saxon, the fucking Prime Minister, and Ianto had voted for him, talk about not fulfilling campaign promises, stands to one side and one glance at his face is enough to tell Ianto that this man is absolutely stark raving bonkers and probably an alien and God why hadn't he seen it before but that's just a side thought because all Ianto can see now is Jack.
Jack, Jack fucking Harkness with the coat and the smile and those goddamn eyes and a body that will never die. He died and then he came back and then he left again and now here he is, beaten and bloody and chained to the wall because he's too dangerous to be left unbound.
Ianto is forced to his knees in front of him and now he realizes why he was treated so well, so he would be left looking perfect and beautiful and like the same Ianto that brought Jack his coffee every morning and shagged him every night and so that when Ianto dies Jack will hurt because it was his Ianto that died and not the wild, feral Ianto that spent the last two months running and running and never stopping and oh God oh God he's going to die, he's going to die, for real this time, there won't be a last minute rescue from fucking Jack in a fucking tractor because Jack is chained to the wall by the fucking Prime Minister.
The cold barrel of a gun is pressed to his temple but it's just left there, and the seconds drag on but he doesn't know how many because he had to trade his stopwatch for a stale bread crust two weeks ago and it's all he can do not to scream for them to just get it over with already and then suddenly there's a hand on his head and it twists and there's a sickening crack from his neck and a loud bang from above his left ear and he has a brief moment to wonder which one killed him first before—
"There's some traces of temporal activity over here," Tosh calls and Ianto kicks through a snow bank to peer over her shoulder through tinted goggles.
"Looks like about a mile and a half that way," he says, pointing upwards.
Owen's face is hidden behind several layers of thick cloth but Ianto can hear the familiar scowl in his voice as he grumbles something about the "fucking Himalayas" and Gwen claps a gloved hand on his shoulder and tells him to "stop being such a prick, Owen, how often do you get to climb Mount Everest" and they start hiking.
That night as they huddle together against the cold (but not like that because even if it is practically in the Torchwood Three job description to fuck one of your teammates that doesn't mean they all have to do it at once) Ianto looks up at the sky screened by clouds and wonders if Jack is up there somewhere, and he wonders if he misses him.