Trouble Is, a Doctor Who + Torchwood Crossover fanfic

I do not own anything. This fic is profitless. -Regular Disclaimer-

I also don't own the title; 'Trouble is' is the name of a song by Allison Iraheta that I was listening to when I started writing. I can't say I normally listen to people like her but she has a good Rock voice.

This story is Ianto-centred and considers a different path for him; one where he does as Jack tells him and kills the partially-converted Lisa. There is a very good chance of a crossover with Doctor Who and I might throw in the odd character from elsewhere.

There will be OCs but their parts will be small and mostly insignificant; I haven't decided on pairings.

Warning: Rating may go up. Bad language used throughout. Slash is likely. Also, I do not like Gwen as a character, there shouldn't be any Gwen-bashing but don't expect a lot of her. Apologies for any OOC (but characters are subjective). Sorry for any bad spelling and grammar; I should get a beta. Hmmm, I think I will.

THANK YOU TO MY BETA, JONESIANTOJONES (who made this readable).

Ianto looked down at the simple form; this paper was going to change his life.

The twenty first century was where it all changes, he knew that and if he were to leave Torchwood, he wouldn't: he would be ignorant to the threats against humanity. Retcon. As soon as he walked out the door, Jack would hunt him down and either retcon him or kill him; neither of which Ianto would look forward to. Ianto had worked for Torchwood for almost five years now and the things he had seen, in the archives of London, in the tunnels of Cardiff's hub, in the holding cells; it was too much. He had seen too much for the retcon to work effectively. Also, the dosage needed to achieve that level of memory loss would almost certainly land him in a coma. No, that was not the way.

It was not like he could stay at Torchwood Three. Seeing what he did everyday, knowing that by trying to save the woman he loved, he had killed three people including the one he was trying to save. Knowing that there was no way he could save Lisa. Looking down the barrel at his love and pulling the trigger. It was easier than he had thought it would be, and that made him sicker than anything else did.

The look of disappointment on Jack's face; the anger on Owen's face; the desire to understand on Tosh's face; and worst of all, the compassion that Gwen exuded. Ianto didn't want her to try and understand because he knew that none of them would ever understand fully. Not even Jack. Ianto had seen the files in the archives and he knew the man was different; that he had been working for Torchwood for over a century. His handwriting hadn't changed and his name was a frequent addition on the reports. Ianto didn't know what the man had been through and frankly he didn't care: he didn't need to know what he had been through to know that the man was a monster.

His suspension had been short-lived: only a couple of days and Ianto had known why he was brought back. He was a butler: clean and make coffee. Then Jack had had one of his worst ideas; he seemed to want to try and include Ianto as they packed for a trip to the countryside: to Brecon Beacons.

Ianto could feel the fear pumping through him, the hope that Tosh had made it to freedom; hoping that the battering he was receiving and his death would mean something. It would be worth it to bring the village to justice, or at least to save her life. Toshiko was the only member of the team that he would miss. They weren't close but unlike the rest of the team she was polite and clean; a nice person.

The drive back in the SUV was murder. The bumpy road causing his tenderised flesh to repeatedly knock against the door of the car. The silence was uncomfortable causing a mixture of drowsiness and the actions of the village to replay in everyone's minds.

Owen would pull through just fine. He had a broken look in his eye and he had already been sick - an action that the rest of the team would never admit to seeing. He would most likely seek comfort in alcohol and sex.

Gwen had never been in a situation like this, and tears still prickled her eyes; her 'compassion' had driven her desire to know why they did it. Ianto envied the fact that she seemed to see the world through rose-tinted glasses and that her naivety had led her to being unrealistically optimistic. She was dropped out of the car not long after Owen: the rest of the team would pretend not to notice when she came in smelling like the medic the next day.

Toshiko wasn't dealing with it well. Unlike Gwen she had known that people were monsters. Ianto knew that she had been imprisoned in UNIT without some of the most basic rights. Yet the smells, the sounds, that scene would remain with her. She was still shaking as she walked up the path to her apartment block struggling with her keys and the lock.

Ianto looked to the driver from the back seat: Gwen had taken the passenger seat for the trip home as she was considered to be in the worst shape, the woman of course loved the attention she was receiving because of it. He and Jack had barely talked since he had been reinstated and it wasn't something that he was looking forward to. The car slowed to a stop once more and Ianto succeeded in keeping in emotionless mask on. "Thank you sir." His voice was expressionless and monotone. He could feel Jack's eyes on his back as he walked to his door, possibly looking to check on him like they had both done to Tosh. Ianto kept his back straight and walked calmly, using all of the control he had not to flinch as each step caused pain to shoot through his body. The Welshman really would be fine: he had already known how horrible people could be and cannibals in the valley could not measure up in any way to the raw terror that the Daleks and the Cybermen had caused. Ianto would get through that all right.

His eyes trailed back over the paper. It had been lying around in his apartment since his suspension, but it was only now, whilst nursing over his cuts and bruises after the longest shower of his life that he was seriously thinking about filling it in. Ianto knew that there was nothing tying him to Torchwood and that this was the only way out that didn't involve him being stuffed into one of the cryogenics chambers or comatose in a hospital. The Welshman started filling out his details: requesting a place as a member of UNIT.

His application was sorted through quickly and this alone painted a nice picture of the fast efficiency of UNIT in comparison to the disorderly Torchwood Three. Ianto was cleared to join UNIT.

Not just that but they seemed to have more of an interest in the man than your average applicant. He was being placed on an advanced course. Ianto knew that they had looked into his past. Personal Assistant to Yvonne Hartman for over two years; experience in the archives in both Torchwood One and Three; one of twenty-seven survivors of Canary Wharf (a number that had decreased by sixteen after a series of suicides); and the only person currently alive who was a member of both branches of Torchwood (Torchwood Two was widely ignored as a 'library' by most). They would want to see what Ianto was like and see if they could reprogram a person who acted well under pressure. See if he could be made into a soldier.

There was only one task left: handing in notice to Jack and telling the man where he was going. It wouldn't be pleasant. Torchwood and UNIT were hardly on the best of terms. Yet deep down, Ianto knew he would slightly enjoy telling his 'Captain' that he was leaving and would never have to see him again.

The day started as any other would. Ianto got into the hub first, barring Jack who was in his office. Tosh would enter, distracted and not looking where she was going, sit down at her desk and tune out the rest of the world in favour of her computer. Owen would thunder through the hub, leaving a trail of mess wherever he touched and ignore the piles of paperwork stacking up on his desk. Minutes later, Gwen would scamper in not making eye contact and pretending that she hadn't just had sex with Owen, then sit in her seat waiting for direction from the Captain.

Ianto would sweep over and clean, make a cup of coffee for each person in the hub and then take up residence in the Tourist Office for an hour, then he would keep repeating these actions. Ever since the Cyberman incident, Jack didn't allow him access to the archives which Ianto had once found home and comfort in.

On his second cup of coffee of the day, he made his rounds and ended on Jack. Instead of leaving however, he remained there, waiting for the Captain's attention. "Yes?" Jack wasn't paying attention as he continued to flick through paper work.

"I'm leaving Torchwood." It burst from the Welshman. As the words left his mouth Ianto knew there were a hundred better ways of saying it but the blunt truth seemed to work just fine.

Jack paused from what he was reading to look Ianto in the eye, deathly serious, "No one leaves Torchwood. Rules and Regulations." He then turned back to the paper in front of him, signalling the end of the conversation.

"Well I am." The Welshman once again regretted the way he chose to say it as the words left his mouth. It wasn't a threat and it held no passion: it was just a statement.

"The only way that you leave Torchwood is with retcon in your system or in a body bag." The man kept his eyes on the paper in front of him but Ianto could tell that he wasn't reading, as his eyes remained stationary. Saying that, you didn't leave Torchwood in a body bag: you remained in the hub in a cryogenics pod forever.

"And I have seen too much and been here for too long. Retcon would most likely be ineffective as there is too much chance of me remembering. That being said, the amount of retcon you would need to use would most likely leave me in a coma." He finished for his boss. "I know sir." The politeness was strained. "The only way out is with royal assent. I have read through many files and scanned the online records. 'Anyone who here for joins the Unified Intelligence Taskforce from Great Britain is acting on behalf of the Crown and has the Monarch's support in leaving any profession he or she was previously part of.'" He quoted the line that had taken him forever to find. It was committed to his memory for long term and Ianto knew that the only way Jack could disagree was by unlawfully killing him there and then. He watched Jack and waited for a response.

The Captain was silent for a good few minutes, and then slowly he said, "Okay." His eyes staring straight at the paper.

Ianto felt a wave of annoyance hit him; Jack hadn't even tried to dissuade him or even argued. At that moment, Ianto felt his lack of worth as part of the team; his leaving meant nothing at all. "I realise that no one has ever elected to leave Torchwood Three but going by Torchwood One's rules of employment, I am required to work two weeks notice." Ianto turned quickly and left the room without another word.

Jack kept his eyes firmly on the paperwork. Ianto was leaving? He couldn't do anything to stop him and he had no control over what was happening. This was a surprise. After the events with the fairies, Ianto had comforted him. He sincerely understood that it was for the greater good: the only one of the team to not be angry with Jack for his decision. After the events in the Brecon Beacons Jack had thought Ianto was finally starting to become part of the team in sacrificing his life for Tosh. He had said that it was his only option to leave Torchwood: did he really want to leave that much? Sure, Owen was mocking; Gwen was patronising; Jack had made him kill his girlfriend. Who was he kidding; Jack was surprised the man had stayed with Torchwood for this long and not tried to kill himself. He supposed the Welshman was resilient.

He had thought that Ianto was coping though. Hell, after the cannibals, Ianto was coping better than anyone else was.

Jack threw his paperwork back down on the desk. He couldn't do anything to stop it.

Sure Torchwood wasn't exactly in line with the law but it was unlawful and stupid for him to try to retcon or kill him.

If he did retcon the boy then he would end up in a coma as he had said or the effects would be cancelled out quickly as life with UNIT was similar to Torchwood. Could Jack kill him? It would be easy to do but it wouldn't achieve anything. Both ways Ianto was no longer a member of Torchwood and Jack did trust the man not to tell anyone about Torchwood. Also, the part of him that liked the Welshman made unnecessarily killing him horrible.

A week passed and the only person he had told about Ianto leaving was Toshiko. She had always seemed closer to him than the rest of the team, maybe it was because they were both introverted; Ianto saving Tosh's life in the valleys had certainly helped. The tech was quiet for the rest of the day; perhaps they were closer than he had thought.

Toshiko played with her lip, her white teeth biting down on them. Ianto was leaving. The constant of the hub; the one who seemed to know what they would need or want before they did; the one that made sure they ate and drank; the one that had risked his life saving hers by head butting a cannibal. She watched him move around the hub fluidly weaving in and out of everyone, cleaning as he went. As he disappeared into the small kitchenette, she shot off towards him.

Toshiko wasn't the most compassionate person. It wasn't that she was cold but her lack of self confidence and poor social skills contributed to a fear of wearing her emotions on her sleeve like people like Gwen. Ianto had noticed this and was, therefore, surprised when he felt her head fall against his shoulder in comfort and her thin, light arms around his frame.

"You're leaving." Toshiko's statement was simple and she didn't need a response as she felt a tear trickle down her cheek. She had never had a close encounter with anyone on the team. Owen had kissed her one New Years but there had been no feeling involved. This was special; this was closeness before she was once again left alone.

The day went by in a blur. She knew she hadn't done anything productive. Toshiko had just spent the time analysing a small bit of alien technology and she still hadn't figured out what it was. She turned to call for Ianto but, as she had just been thinking, he seemed to know what she needed before she did. The Welshman was already walking towards her. "Archives?" She would miss how he did that.

"Yeah, it is fine to hold." Toshiko picked it up to demonstrate her point. There was a time when Ianto hadn't been allowed in the archive but no one seemed to know where anything was so Jack had reinstated his duty. As his skin made contact with the small circle of alien technology, Toshiko saw a blinding light and heard Ianto howl in pain. Apparently it wasn't 'fine to hold'.

As the light cleared, there was no longer a Ianto, there was no longer a hub. All around her she could feel the pain and fear. Bodies littered the floor of the narrow hallway. Her feet carried her forward without her mind functioning. Up ahead she could see a familiar face: Ianto.

"Ianto!" She screamed his name, scared, but received no reply.

The man she knew looked right through her, she noticed people behind him. "Get down to the archives. Head to the back wall. In the right corner there is a hidden room. Key in one - three - five - two. It won't hold much fire, definitely nothing from the Daleks but hopefully they won't know you are there." His voice was strong. As she saw the people running down the stairs, Toshiko understood what was happening. Canary Wharf.

A lone man remained stood with Ianto. He was short but a very plump man; ageing with his hairline receding. "Ianto, come down with us. You can't survive up here."

"Go downstairs Kev. I've got to find Lisa. Keep everyone calm." Ianto left the man quickly and Tosh could see the look in his eye. This was a goodbye; Ianto wasn't expecting to see him again. He was effectively walking into Hells mouth for the woman he loved.

Toshiko followed the young Welshman as he pulled out a small pistol. He looked at it faintly and she could tell that he was assessing the situation. In the middle of a war between two metallic forces the small pistol was useless: he just had to pray he would be lucky. A long shot.

Ianto made his way up the cold, clinical staircase. He needed to get to Floor Nine: Human Resources, where Lisa worked. Ianto darted up the stairs with Tosh following after him, until she saw him freeze. The tech could feel fear flood the area as she looked up. One Cyberman blocked the way.

Toshiko had never seen one alive and moving before. The partially converted Lisa did not compare to this thing. "You will be upgraded." The haunted, robotic voice announced. Toshiko had seen a lot of things in her life but the pure terror she felt was on a level it had never before reached.

The Cybermen must have needed more bodies to convert because the metallic beast didn't shoot at the Welshman. It mechanically descended down the stairs that separated them. Ianto saw his chance, and aiming at the foot of the machine shot a rapid succession of bullets that was enough to disfigure the foot and leave it useless. The robotic body lost its footing and plummeted down the stairs landing in a heap.

The Welshman was finding it hard to keep his breathing regular and though most would remain frozen in fear he knew he had to move. Ianto knew that the Cyberman was by no means finished off so he moved as fast as his feet could carry him up the floors until he saw the large '9' directly in front of him.

Lisa: Ianto had only one thought as he was running through the floor. She wasn't anywhere; he couldn't find her. She couldn't have gone for shelter: if so she would have headed to the archives... That meant she was... that they took her and... Tears flowed down the man's face as he ran for the staircase once more. He wouldn't believe it until he had seen it with his own eyes. Lisa was alive and well. She was just waiting for him.

Toshiko tried to follow after him and she managed for the most part, but what happened was a blur. Suddenly, hundreds of Daleks inhabited the sky yet before anything else could happen they were gone. There was an eerie silence. Tosh knew that this anti-climax was the end of the war: she could feel it deep down. If anything, Ianto was even more rushed. Where was Lisa? The Welshman continued to thunder up the steps. The woman lost him once more.

She was drawn to the room by the sound of strangled sobs. There, as she walked in, was an image that would stay in her mind forever.

An elegant body lay battered and maimed on a cold metallic table. The gleam of metal shining from different parts of her body. She lay unmoving: dead to the world.

Collapsed against the opposite wall, his legs drawn close to his body, rocking slowly, was the source of the noise.

The world faded into a pitch black and all Toshiko could hear was a deep, heavy breathing.

The small boy was curled up in his bed; eyes squeezed tightly shut and head buried under his pillow. If he didn't see it, didn't hear it, then it didn't happen. Too bad that the world didn't work like that. He could hear a woman scream; his Mam. She had long ago told him to shut himself in his room when Tad was like this and not to make any noise.

The boy heard a dull thud that came from much closer: his sister's room. The boy opened his eyes: ice blue. They carried an experience; they had lost their innocence and that look was alien on a seven-year-old boy. This had happened so often before. Toshiko saw the beginnings of tears prickling at the boy's eyes as he rose from his bed and moved to the other side of the room.

He heard his Tad's heavy footfalls as he took a deep breath. He slid his book off the shelf and watched as it collided loudly with the floor.

There was a momentary pause before the door was thrown open. Silhouetted by the light was a large frame: Bald, tall, and bulky.

Toshiko stood in silence with tears flowing freely down her face, unable to look away as the man's fist connected to the child repeatedly and savagely. The boy's eyes slid out of focus soon after. He didn't fight back - he couldn't.

Toshiko's sight once again faded to a jet black though the heavy breath was still haunting her ear.

Toshiko saw her back leaving: running out of an open doorway. The clear plastic hanging from the walls flapped in the wind. The ever-lingering, metallic scent of blood filled the air. She saw her saviour get pushed roughly to the ground; heard him grunt as the butt of a gun slammed into his chest. Then the sickening crack as it slammed against his head. Ianto's eyes were still faintly open: he still stirred. The woman: the beast. It continued to bring down forceful hits with the weapon. Tears threatened Toshiko once more as she saw Ianto struggle not to cry out in pain.

Toshiko felt helpless as she watched the beast continue to batter her friend; as it shrieked in high-pitched laughter; as Ianto fought to keep consciousness. How the woman finally stopped her assault only to gag him tightly with thick rope and through a sack over his head. How Ianto lapsed into unconsciousness.

The familiar sight of the picture darkening left Toshiko hearing only that heavy breathy once more.

This scene she knew well. The Hub. Yet, it was different. Darker: more eerie: full of despair. The dim blue hue partially lit the expansive room. A single figure stood silhouetted - a man frozen in horror. Ianto's eyes were red and tears glazed his skin as they fell. He looked at the scene in front of him: Lisa's partially converted body lay lifeless on the floor but this girl, a different girl stood in front of him.

Her face was disfigured; the top of her head had been slashed and reattached haphazardly. Her features lit by the bright smile she donned. Her eyes shimmering as words escaped her. "Come on Ianto, now we can be converted together."

Ianto stammered, disbelieving. How could his Lisa have done this? She was always kind-hearted: so gentle.

His voice was cracked as he spoke, his voice overflowing with sentiment. "I love you." He didn't break eye contact as he slowly lifted his right hand - accurately positioning the pistol so it would kill in one shot, put her out of her misery. "I'm... I'm so sorry." He pulled the trigger and watched as his love fell to the floor: motionless as life slipped away from her.

Oxygen flooded Toshiko's lungs. The light blinded her. Ianto's screams of pain filled her ears. Suddenly it was over. She was back in the hub; stood in front of a heavy-breathing Ianto with the rest of the team staring at them. She felt faint and weak. Then, not for the first time, everything went dark.

Jack darted forward but he was too late, she was already falling. Luckily Ianto was close enough to pull her limp body into his arms. She was covered in sweat and tears stained her cheeks.

Closer inspection from Owen found that she was unconscious and would be fine by the time she came to, but what Jack wanted to know was what happened. As he asked the Welshman, Ianto pointed to the artefact that had fallen to the floor in the encounter.

"I was talking to Tosh and she handed me the artefact: when both of us were touching it, a bright light came from it and it felt like my brain and eyes were burning. I'm not sure what happened to Toshiko but she looks like she has been crying and her tears have dried; there shouldn't have been enough time for that to have happened so I am guessing that she was out of time." The Welshman wouldn't look the Captain in the eye; he hadn't since he resigned. Whenever he did he felt a rage burning through his being.

It was at that point that Tosh stirred; Gwen and Owen had since left on a "Weevil Hunt" though Ianto was fairly certain that it was just an excuse to leave for sex. The petite Japanese girl slowly opened her eyes blinking several times to get used to the light. As she looked up she noticed Jack and Ianto were sat near to the sofa she was sprawled out on. Before she could stop herself she let her maternal nature dominate as she squeaked, "Ianto" and enveloped him in a warm hug.

Ianto's eyes widened in surprise. It was rare to get hugs of comfort in this line of work: two in a day was unheard of. It was starting to seem awkward. He pulled the girl close. Supplying her with warmth as she sobbed into his shoulder. Before he could get the chance to ask what had happened, the Captain had.

"I... I could -could see things from the past. From Ianto's past. I -I was there. Stood with him as he went through it but I couldn't do anything. Ianto." Toshiko was openly crying and the last word was said with such emotion that it made Jack want to know what she had seen to make her like this. Know what Ianto had been through. Jack noticed that Ianto had grown much more rigid. This time he was not only avoiding the gaze of the Captain but his friend as well. He seemed to be regretting that his friend had had to see it and judging from the sharp movements of eyes, Ianto was wondering what in his past Toshiko had seen and formulating ways to avoid the conversation he guessed was going to occur.

As Toshiko loosened her grip on the archivist, he couldn't get away fast enough. He was polite about it but was clearly spooked, leaving to make coffee so as to get out of their presence.

Jack watched as the Welshman kept his head down. His skin was pale as he started pressing the buttons of his beloved coffee machine and he could see Ianto's hands shaking. After the Lisa incident, Jack had rechecked the man's file. It was pretty much empty just as it had been when Ianto had begun to stalk him in search for a job. At both times, he had just thought that Ianto had led a perfectly average life; just unfortunately not having any relatives alive and well. Now, Jack was wondering whether Ianto had doctored his criminal record and medical records to make sure that his past was well veiled. He handled the computers almost as well as Tosh; he obviously had no qualms about keeping his colleagues in the dark and throughout his career in Torchwood Three he had shown a very clear talent in making people disappear. He was just one of the many. Jack supposed it should have been obvious but Ianto had a clear talent in hiding things; he so often sank into the background that Jack had forgotten about him and overlooked him several times.

Gwen and Owen barging in broke the unsure atmosphere, both oblivious as to what had just happened. Unsurprisingly they didn't have a weevil with them. The rest of the day passed quickly, Ianto resigning to the archives for comfort and solitude.

His last days at Torchwood Three were spent avoiding everyone: Gwen and Owen still didn't know he was leaving and ever since Tosh's trip through his memory lane, both she and Jack had been trying to talk to him. His evasion techniques were too good for them. In the time he would normally spend cleaning and making coffee for them, Ianto had drawn up detailed plans, with labelled sketches, of the archives. They were fool proof. However, hopefully a fool wouldn't be in his archives; that was why he was leaving the plans with Toshiko. She would be the one that needed them most and he would be damned if he left any of the other in his archives: they had the collective organisation skills of a dead rabbit.

So, on his last day, he ignored his usual day schedule and singled out Tosh. She seemed to understand that he had been avoiding the topic of what she had seen so played along and didn't mention it. He commandeered the Conference Room where he had shown Toshiko the detailed plans. There were more expanses of archives than any other part of the hub, so it was a long task. He was interrupted by the Captain who threw open the door and pushed his way inside. "What's going on?"

Jack didn't like being left out of the loop; Ianto had long known this and therefore wasn't surprised by the question. "I'm showing Tosh the plans of the archives and how to catalogue the artefacts so one of you knows how to find things after today."

Jack Harkness paused momentarily before speaking. "Toshiko has enough to do; why don't you show me or Gwen?" It wasn't really a question. Jack noted that Ianto still refused to look him in the eye.

"Because I only just finished drawing up the plans so I only have a short time to explain it; so I chose the person who would understand how I have ordered the archives." Ianto took a short breath. "Also, Toshiko will be the one in need of the archives the most on the team as she works with the artefacts more often than the rest of the team." Ianto effectively, but politely, insulted Jack's intelligence.

Jack remained silent not knowing how to answer that.

"And if Toshiko is in charge of them, they are more likely to stay orderly." Ianto looked to his fob watch for the time. He looked to the Tech. "Do you want to go down to the archives now?" As he received a nod from the girl the two walked straight past the Captain.

That day, Ianto left. No party. No celebration. Only a teary goodbye from Toshiko. Gwen and Owen either didn't know or didn't care that it was his last day; he would guess both. Jack hadn't said anything since he walked into the conference room. His last day as a member of Torchwood Three was an anticlimax. Toshiko pulled him into a comfortable hug and at the end of the day, they parted ways, tears welling up in the girl's eyes. As he walked away from the hub to his already packed apartment, Ianto wondered if he would ever see the people that he had just left behind again. Was this really his last dealings with Torchwood Three?

I don't know what is going to happen but this won't be the last time you see Torchwood. Hell, he won't be gone for that long I don't think. There will probably be more Owen in those chapters.

This is a Ianto-based fic; expect a lot of him and other character only in moderation. A familiar red-head should be making an appearance soon. This will go along with the Who-verse timeline for the most part, there might be some slight mistakes and blurs in the timeline but it should be accurate for the most part. Know that I am a big Ianto fan and will make the character very significant to a lot of events; obviously not wanting to take away the limelight from others, he won't be a God or anything.

Reviews appreciated.