These fics are AU (i.e. alternate universe). While someone could say all of fanfic is AU what you can find here are those fics that are notably AUs.
A Day in the Life by kausingkayn
Genre: angst, AU
Summary: A day in the life of Ianto Jones; boyfriend, newspaper editor, serial killer.
Sequel:
Behind Blue Eyes
Warnings: Child abuse, detailed murder, character death
Summary: Ianto Jones lives a very meticulous life. He has a schedule for everything he does - breakfast, work, personal time, love life, and his murder of the month. But when something goes wrong and one of his victims becomes the Cardiff police's latest case, will he be able to keep his personal life a secret? Not if Jack Harkness, consultant to the police and boyfriend of Ianto Jones, has anything to say about it.
As You Wish by choccy-grl
Notes: Written for bookwrm89’s xmas challenge to write a story based on her header located here
Blood and Roses by choccy-grl
Summary: The Doctor’s in town again. Oh and there’s moonlight, a river and a long stemmed rose.
Blood Ties by smilla840
Warnings: Incest, claiming. I repeat, INCEST. Of the Jack/Ianto variety, which means AU, obviously. And slash. Also very vague spoilers for 2x12.
Notes: Even if it's AU, it sticks close to canon up to 'Cyberwoman'. Actually I always thought it would be fun to write a Jack/Ianto incest fic - it's *Torchwood* and I'm weird like that, and I read too much Wincest lol! I even came up with an idea a few months ago that had Jack and the Doctor and Jack's two missing years, except that I can not for the life of me remember anything else about it XD So that's something else! Hopefully you haven't all run away by now... ;)
Codename: Victory by moonfirefic
Summary: Ianto Jones has been searching for information about who he is his entire life. Canary Wharf gave him some answers and a whole new set of questions.
Get Jones by valderys
Notes: AU for the Age of Steel Whoniverse, this is just one take on what other paths Ianto and Jack may have taken :)
Summary: JACK: Ianto Jones, born August 19th 1983. Able student but not exceptional, one minor conviction for shoplifting in your teens. But what if crime had suited Ianto?
Harkness and Jones by 0lizzybennet0
Genre: Drama, Romance
Summary: Somehow Jack had ended up with a quiet Welsh man in his house
Human Nature by missthingsplace
Warnings: AU, Slash, angst, humour, fluff
Summary: When a new boy arrives in his class in his final year of high school Ianto Jones world is knocked out of kilter ...
Just Antoher Heart in Need of Rescue by rietta
Warnings: Do not try this at home! I will not be held responsible for any damage to vehicles that occur as a result of this fic.
Summary: AU. Ianto is a tailor, resourceful as ever; and Jack is doing what Jack does best: saving people.
Kissing Ianto Jones by madder-rose
Summary: Request!Fic for astuta and based on the movie Kissing Jessica Stein, Ianto Jones responds to what he thinks is a personal ad in the women’s section of the paper. Little does he realize that the person who posted the ad is attractive, funny and desperately lonely Jack Harkness who’s anything but a woman.
Long Ago (and Far Away) by madder-rose
Warnings: none
Summary: In WW2, 1942, Captain Jack Harkness is in hospital. Ianto Jones is his stubborn physical therapist who finds himself falling for his equally stubborn patient.
Sequel:
Bluebirds
Summary: Wherein, while World War Two rages on, Captain Jack Harkness, the grouchy bastard, moves in with physical therapist Ianto Jones, the man with the patience of a saint and things are awkward. Wherein they both acquire a lodger and Jack solves the mystery of a strange military plot , and discovers he is not as entirely useless as he thought.
Love Will Tear Us Apart by athousandfics
Warnings: Slightly cracky, slash, language.
Summary: Why leaving Owen alone with alien tech is a supremely bad idea...
Mage!verse by gracie-musica
Warnings: AU like whoa
More Than Flesh and Bone by lucyjanesparlor
Warnings: No spoilers. Pre-series.
Summary: Everyone has one night that changed their lives forever. Ianto's got a few.
Not the Normal Way by butterflycell
Warnings: fluff; AU like WHOA; smut
Summary: Jack Harkness had never been good at spotting the little things, but that was okay, because his friend, Ianto Jones, hadn't either. The little things had been left unnoticed since university, but they were starting to appear several years down the line.
Route 412 by jerbearthompson
Notes: For Elle! Because she wanted something really Jack/Ianto-y. And I get really bored on the bus and think up somewhat crazy AU ideas. Hazzah. I based it around that not-so-famous Eagle vs. Shark quote, "I have two things to say. One: I am leaving tomorrow on a bus. Two: that could change."
Summary: Ianto was on the bus when it happened. There was a sharp swerve, and then a warm body was falling down on top of him.
Silent Running in Deep Waters by choccy-grl
Notes: AU Set during the Second World War.
Summary: Disgraced American pilot Captain Jack Harkness starts again in a new country and a new service but will a young sonar operator make things easier or harder for Jack?
Silver Service by a-silver-story
Warnings: M.M, rentboy!Ianto, brief Het, Alternate Universe
Summary: Started as a PWP, but since it's me (sorry folks!) and I really can't do things by halves, it grew and grew and grew (and not in an innuendous sort of way). Doctor Smith owns a posh Cardiff hotel, and the respectable Sixth Earl of Boeshane is coming to stay - and he brings with him some very specific demands.
Strange and Changing by dizzydame
Warnings: AU but minor spoilers through Journey's End.
Suspension by plotbunniesinc
Notes: Season 1 only – This is our Post-Cyberwoman fic!
Summary: Every decision made changes the future. For better or worse, Ianto wakes up in a universe where he never had a chance to hide Lisa in the basement – A universe where he died in the wreckage of Canary Wharf and somebody else went to Cardiff with a deadly secret...
The Torchwood Patient by lucyjanesparlor
Warnings: Spoilers for Doctor Who episodes "Army of Ghosts" and "Doomsday", Torchwood episodes "Captain Jack Harkness" and "Everything Changes."
Summary: What if Ianto brings back a very different secret with him from Torchwood One?
Through Other Eyes by halfspokenwords
Summary: An AU in which Ianto is offered command of Torchwood Three after Canary Wharf. Written for tw_exchange.
Torchwood House by cazmalfoy
Notes: This is AU - Not much of a shock there, then.
Summary: Welcome to the Torchwood Institute, a school for those blessed with extraordinary talents...
Triple-Lattè by jerbearthompson
Notes: So I blame this entirely on Ostin, who was telling me how his boyfriend and his boyfriend’s female roommate act like more of a couple than they do. He also requested Australian nicknames and Elle prompted: Cafe, photos, shoes. But… I kind of forgot about the last one. I’ve been watching far too many sappy movies lately. And why oh why do I always have to write Jack pining over Ianto? I keep coming back and adding notes here, I should stop. Another one: I live in Australia, so I made up all the names of shops. Research is too hard. Last note: Another one of those stories that don't run so smoothly but my mind is rather shot right now. That's all, I promise.
Summary: Jack laughed, because he was expected to, because it was so obviously a joke. He wondered if Ianto could tell it was fake.
Tsar of Torchwood by beth-mccombs
Warnings: none, just the usual agnst. I may be bordering on fluff here. For Thrace, I believe this is a four on your scale.
Summary: It's Christmas Eve and Ianto makes a startling confession about his past to Jack.
Where I Belong by remuslives23
Warnings: m/m sex, m/m/f sex (mild), threesome, infidelity (of sorts), angst, language, AU.
Summary: There is a time for departure even when there's no certain place to go' - Tennessee Williams.
Where Would We Be? by everlongsplace
Warnings: MalexMale pairing, angst, swearing, adult chapters contain exlicit sexual references.
Summary: AU. Jack falls for Ianto while he's still dating Lisa and is desperate for him to leave her so they can be together. Things become more complicated for them when Jack is forced to hire Lisa to work for TW3.
You and Me and the Satellites by lucyjanesparlor
Notes: What if . . . post-Cyberwoman, Jack retcons Ianto and he leaves for a new, Torchwood-less, life. But Jack can't forget and can't let go.
Summary: "Is that what Torchwood did to him? Is that what we did? We took away that smile."
A Day in the Life by kausingkayn
Genre: angst, AU
Summary: A day in the life of Ianto Jones; boyfriend, newspaper editor, serial killer.
Sequel:
Behind Blue Eyes
Warnings: Child abuse, detailed murder, character death
Summary: Ianto Jones lives a very meticulous life. He has a schedule for everything he does - breakfast, work, personal time, love life, and his murder of the month. But when something goes wrong and one of his victims becomes the Cardiff police's latest case, will he be able to keep his personal life a secret? Not if Jack Harkness, consultant to the police and boyfriend of Ianto Jones, has anything to say about it.
As You Wish by choccy-grl
Notes: Written for bookwrm89’s xmas challenge to write a story based on her header located here
Blood and Roses by choccy-grl
Summary: The Doctor’s in town again. Oh and there’s moonlight, a river and a long stemmed rose.
Blood Ties by smilla840
Warnings: Incest, claiming. I repeat, INCEST. Of the Jack/Ianto variety, which means AU, obviously. And slash. Also very vague spoilers for 2x12.
Notes: Even if it's AU, it sticks close to canon up to 'Cyberwoman'. Actually I always thought it would be fun to write a Jack/Ianto incest fic - it's *Torchwood* and I'm weird like that, and I read too much Wincest lol! I even came up with an idea a few months ago that had Jack and the Doctor and Jack's two missing years, except that I can not for the life of me remember anything else about it XD So that's something else! Hopefully you haven't all run away by now... ;)
Codename: Victory by moonfirefic
Summary: Ianto Jones has been searching for information about who he is his entire life. Canary Wharf gave him some answers and a whole new set of questions.
Get Jones by valderys
Notes: AU for the Age of Steel Whoniverse, this is just one take on what other paths Ianto and Jack may have taken :)
Summary: JACK: Ianto Jones, born August 19th 1983. Able student but not exceptional, one minor conviction for shoplifting in your teens. But what if crime had suited Ianto?
Harkness and Jones by 0lizzybennet0
Genre: Drama, Romance
Summary: Somehow Jack had ended up with a quiet Welsh man in his house
Human Nature by missthingsplace
Warnings: AU, Slash, angst, humour, fluff
Summary: When a new boy arrives in his class in his final year of high school Ianto Jones world is knocked out of kilter ...
Just Antoher Heart in Need of Rescue by rietta
Warnings: Do not try this at home! I will not be held responsible for any damage to vehicles that occur as a result of this fic.
Summary: AU. Ianto is a tailor, resourceful as ever; and Jack is doing what Jack does best: saving people.
Kissing Ianto Jones by madder-rose
Summary: Request!Fic for astuta and based on the movie Kissing Jessica Stein, Ianto Jones responds to what he thinks is a personal ad in the women’s section of the paper. Little does he realize that the person who posted the ad is attractive, funny and desperately lonely Jack Harkness who’s anything but a woman.
Long Ago (and Far Away) by madder-rose
Warnings: none
Summary: In WW2, 1942, Captain Jack Harkness is in hospital. Ianto Jones is his stubborn physical therapist who finds himself falling for his equally stubborn patient.
Sequel:
Bluebirds
Summary: Wherein, while World War Two rages on, Captain Jack Harkness, the grouchy bastard, moves in with physical therapist Ianto Jones, the man with the patience of a saint and things are awkward. Wherein they both acquire a lodger and Jack solves the mystery of a strange military plot , and discovers he is not as entirely useless as he thought.
Love Will Tear Us Apart by athousandfics
Warnings: Slightly cracky, slash, language.
Summary: Why leaving Owen alone with alien tech is a supremely bad idea...
Mage!verse by gracie-musica
Warnings: AU like whoa
More Than Flesh and Bone by lucyjanesparlor
Warnings: No spoilers. Pre-series.
Summary: Everyone has one night that changed their lives forever. Ianto's got a few.
Not the Normal Way by butterflycell
Warnings: fluff; AU like WHOA; smut
Summary: Jack Harkness had never been good at spotting the little things, but that was okay, because his friend, Ianto Jones, hadn't either. The little things had been left unnoticed since university, but they were starting to appear several years down the line.
Route 412 by jerbearthompson
Notes: For Elle! Because she wanted something really Jack/Ianto-y. And I get really bored on the bus and think up somewhat crazy AU ideas. Hazzah. I based it around that not-so-famous Eagle vs. Shark quote, "I have two things to say. One: I am leaving tomorrow on a bus. Two: that could change."
Summary: Ianto was on the bus when it happened. There was a sharp swerve, and then a warm body was falling down on top of him.
Silent Running in Deep Waters by choccy-grl
Notes: AU Set during the Second World War.
Summary: Disgraced American pilot Captain Jack Harkness starts again in a new country and a new service but will a young sonar operator make things easier or harder for Jack?
Silver Service by a-silver-story
Warnings: M.M, rentboy!Ianto, brief Het, Alternate Universe
Summary: Started as a PWP, but since it's me (sorry folks!) and I really can't do things by halves, it grew and grew and grew (and not in an innuendous sort of way). Doctor Smith owns a posh Cardiff hotel, and the respectable Sixth Earl of Boeshane is coming to stay - and he brings with him some very specific demands.
Strange and Changing by dizzydame
Warnings: AU but minor spoilers through Journey's End.
Suspension by plotbunniesinc
Notes: Season 1 only – This is our Post-Cyberwoman fic!
Summary: Every decision made changes the future. For better or worse, Ianto wakes up in a universe where he never had a chance to hide Lisa in the basement – A universe where he died in the wreckage of Canary Wharf and somebody else went to Cardiff with a deadly secret...
The Torchwood Patient by lucyjanesparlor
Warnings: Spoilers for Doctor Who episodes "Army of Ghosts" and "Doomsday", Torchwood episodes "Captain Jack Harkness" and "Everything Changes."
Summary: What if Ianto brings back a very different secret with him from Torchwood One?
Through Other Eyes by halfspokenwords
Summary: An AU in which Ianto is offered command of Torchwood Three after Canary Wharf. Written for tw_exchange.
Torchwood House by cazmalfoy
Notes: This is AU - Not much of a shock there, then.
Summary: Welcome to the Torchwood Institute, a school for those blessed with extraordinary talents...
Triple-Lattè by jerbearthompson
Notes: So I blame this entirely on Ostin, who was telling me how his boyfriend and his boyfriend’s female roommate act like more of a couple than they do. He also requested Australian nicknames and Elle prompted: Cafe, photos, shoes. But… I kind of forgot about the last one. I’ve been watching far too many sappy movies lately. And why oh why do I always have to write Jack pining over Ianto? I keep coming back and adding notes here, I should stop. Another one: I live in Australia, so I made up all the names of shops. Research is too hard. Last note: Another one of those stories that don't run so smoothly but my mind is rather shot right now. That's all, I promise.
Summary: Jack laughed, because he was expected to, because it was so obviously a joke. He wondered if Ianto could tell it was fake.
Tsar of Torchwood by beth-mccombs
Warnings: none, just the usual agnst. I may be bordering on fluff here. For Thrace, I believe this is a four on your scale.
Summary: It's Christmas Eve and Ianto makes a startling confession about his past to Jack.
Where I Belong by remuslives23
Warnings: m/m sex, m/m/f sex (mild), threesome, infidelity (of sorts), angst, language, AU.
Summary: There is a time for departure even when there's no certain place to go' - Tennessee Williams.
Where Would We Be? by everlongsplace
Warnings: MalexMale pairing, angst, swearing, adult chapters contain exlicit sexual references.
Summary: AU. Jack falls for Ianto while he's still dating Lisa and is desperate for him to leave her so they can be together. Things become more complicated for them when Jack is forced to hire Lisa to work for TW3.
You and Me and the Satellites by lucyjanesparlor
Notes: What if . . . post-Cyberwoman, Jack retcons Ianto and he leaves for a new, Torchwood-less, life. But Jack can't forget and can't let go.
Summary: "Is that what Torchwood did to him? Is that what we did? We took away that smile."