A/N: I know the first few paragraphs of this are terrible. They move incredibly fast and they tell rather than show. That is done of purpose. I need to get the background information out of the way. You can just skip these paragraphs and go to the end of the flashback if you don't want explanations on what Martha's been doing since the 456 incident.
This is strictly AU. It's Doctor Who cannon up until the end of "The Planet of the Dead" (first 2009 special). It's Torchwood cannon up until the end of the "Children of Earth" arc (season 3, 2009). It's Death Note cannon up until L's death, but more about that will be revealed later. Things will happen that most likely will not fit cannon after these episodes (except for Death Note, because it's done). I have also shifted Death Note's timeline ahead a couple decades. Yagami Light doesn't find the Death Note until 2023.
Also, English names will be written "Title First_Name Last_Name", as usual (e.g. Captain Jack Harkness). Japanese names will be written "Title Family_Name Given_Name" following Japanese convention (e.g. Chief Yagami Soichiro).
The office of Torchwood filled with the unfamiliar sound only two members would recognize. One of them, luckily, was in the office that very moment. Martha Jones had joined Torchwood after she got back from her honeymoon. She had been quite surprised to see the Torchwood 3 office in Cardiff destroyed, but began tracking down employees immediately. She knew Owen and Toshiko had died. That left Jack, Ianto, and Gwen. Jack, she lamented, is near impossible to be found. She decided to start with Ianto. Ianto's apartment was vacant. A quick internet search showed him on the list of the dead from the 456 incident. That left Gwen.
"Martha Jones! Come in," Gwen said as Martha arrived at her apartment.
"I'm here about Torchwood."
"Oh. Well Torchwood is gone."
"I noticed the office downtown was gone. What happened?"
"The Hub was destroyed during the incident with the 456. Shortly after the government ordered the execution of Torchwood employees."
"It's a long story."
"I've got time."
Gwen filled Martha in on all the details of the incident. In the end they decided to rebuild the Hub, and lead Torchwood 3, along with Rhys, until Captain Jack could be found.
That was what Martha was doing when the sound of the T.A.R.D.I.S. filled the office. Actually, they where still in the process of clearing out the debris. They still had no clue on how to get the actual rebuilding done. Hopefully an alien device Jack hid away would help with that. Gwen and Rhys had stepped away for lunch. Martha quickly located the materializing blue box and waited until the Doctor, number ten, stepped out.
"Nice S.E.P. field," he commented.
"Martha? What are you doing here?"
"I decided to leave U.N.I.T. shortly after the incident where the Earth was stolen. But I just joined Torchwood 3. We're in the process of cleaning up the mess from the 456 incident."
"The 456 incident? Oh, yeah. I forgot about that. Nasty piece of work they are. The universe's drug junkies, the whole lot of them. I've never personally met one, and I'm hoping to keep it that way."
"Anyways, what are you doing here?"
"I'm looking for Jack. Is he going to be back soon?"
"Jack? He teleported away."
"He did what? How many times do I have to disable his toy. Alright, come on Martha, let's go get him."
"We're getting Jack. I need him for where we're going?"
"And I'm going because?"
"A medical doctor might be good. Even in Jack's case, a deadly heart attack is nothing to laugh at."
"A heart attack, are you planning many of those?"
"Where we're going, it's a reality. Talking about which, we need a mask for you and a fake name. The fake name is easy, the mask, less so. Let's see, I think Jack had a holographic projector somewhere." The Doctor starts opening and rifling through the safe, with the help of his Sonic Screwdriver. "Ah yes, here it is. And with a few modifications, presto! A holographic mask. Good for protecting one's identity from a murderous psychopath."
"Doctor, can you tell me what's going on?"
"Afraid I can't. Not yet, anyways."
"I don't like repeating myself twice. Everything will be explained after we pick up Jack."
"And how are we going to find Jack?"
"Luckily I installed a tracking device in that toy of his. As long as he hasn't fixed time transport..."
"You should be able to track him?"
"Correct. To the T.A.R.D.I.S.!"
"Wait, what about Gwen and Rhys?"
"I'll get you back before they even realize you're gone."
"Okay, lets go then."
Finding Jack was easy. He was on a deserted planet, presumably in self-exile. He leaped at the chance when the Doctor told him he could save thousands of lives.
"Welcome to Tokyo, Japan, Earth, year 2031. The Earth is under the rule of a man called Kira. Martha, put on your mask before we go out. If you are asked a last name, claim it is Smith. That should be safe enough. Jack, don't conceal your name. But if you have a heart attack, act dead until it is safe."
"Will you tell me what is going on?" asked Martha, bewildered.
"Oh, right. I should tell you, before we go out. It's not safe out there. In the year 2023, a man named Yagami Light, just a senior in High School, found an artifact called the Death Note. It allowed him to kill anybody with just a name and a face. The Death Note is a device used by some inter-dimensional beings called Shinigami. Anyways, Light started using the Death Note to kill criminals, not minor offenders, but people convicted of major crimes like murder and rape die of a heart attack."
"That's terrible! I mean, these criminal were probably already sentenced to death, but no one should be able to circumvent the law like that!"
"Some criminals were killed before they where even arrested. Some had never even been convicted."
"Then why are we in the year 2031?! Shouldn't we be in 2023 trying to stop this bastard?"
"It's not my place to interfere with events. Especially events that shape the future of the human race."
"Why are we here then, Docor?" It was Jack this time.
"Let me continue on with the story. Soon the U.N. notices the attacks and calls upon a detective named L. I'm not sure why U.N.I.T. wasn't called, but that's beside the point. L pinpoints the attacks to Tokyo and through various methods begins to suspect Light of being the killer, now called Kira. Light outsmarts L though, and L eventually lets him free. L gets killed, the reason is unclear, but all evidence points to Shinigami intervention. Anyways, at that time Near and Mello get involved in the case. Eventually Near catches Light/Kira and that's the end of it. The Death Notes are destroyed and the world goes back to mostly normal."
"But you said the Earth is under Kira's control." It was Martha again
"That's correct. The timeline has been tampered with. We need to locate the tampering and stop it, or the whole future of Earth will be changed."
"And so why are we here and not at the area where the tampering took place?"
"Good question. I don't know when the tampering took place. We are here to locate that information. The case should have been closed by now, so we can backtrack the deviations. It is also soon after the start or Kira's global reign, so their are still some places of information. Right now we are in the headquarters of a rogue group called the SPK. They were originally formed by the President of the United States to track down Kira, but the President shut them down after the U.S. approved Kira's rule. Instead of dissolving, the SPK moved outside the governments control. They are considered outlaws right now. Hopefully the tampering to the timeline hasn't removed them totally. Though I doubt Near is in charge. Now let's get out of here. Move slowly with your hands up. And Martha, didn't I tell you to get your mask on?"
As the Trio exited the T.A.R.D.I.S., guns pointed in their direction. "Explain why you are here," a blond, tough-looking man in a business suit demanded.
"Ah, you must be Anthony Rester. Or at least, that's your alias. I won't reveal your real name. I'm the Doctor, this is Martha Smith, and this is Captain Jack Harkness. Am I correct in assuming this is the headquarters of the SPK?"
"It is. Nice to see you again, Doctor." Said a hunched over black haired figure.
"L! You're alive?"
"Why wouldn't I be?"
"Well, according to my information you died investigating Kira in 2004, shortly after the Yotsuba incident."
"Wait, did Light kill me, or was it Misa? Or maybe one the other Kiras?"
"It was a Shinigami, I think. The history books don't really say."
"The Shinigami was probably Rem, the owner of the Death Note we found in the Yotsuba incident. He disappeared shortly after that, we are not sure why. Light got close to discovering my name, I think Misa has the eyes, so I hightailed it out of their. So are you saying Rem's disappearance saved my life?"
"His disappearance sacrificed many lives. The Kira case was suppose to have ended in Light's death in 2030. Your successors Near and Mello caught him."
"Successors? I thought I had decided on Near."
"You hadn't yet."
"Right. I didn't do that until 2025."
"And now I have to go."
"2024. I'm sorry, L, but you have to die."
With that the trio got in to the T.A.R.D.I.S. and it started to disappear.