Author's note: The Indigo Stain is the second episode of a fan fiction version of Sherlock's Series 3. The first episode is "The Silver Blaze Revival." The next episode is episode three, "The Uncanny Valley," which is followed by the fourth and final episode, "Four Elizabeths."

Warning: This episode includes references to child abduction, miscarriage, and various medical disorders.

Spoilers: This story may contain spoilers for all episodes of Sherlock (BBC) through s02e03 "The Reichenbach Fall."

Sherlock Holmes had died, washed up, and left London in one day. He returned, briefly, just after his funeral, covered gracefully by his ever trusty Homeless Network. He returned for various reasons, the most obvious being to verify the survival of John, Mrs. Hudson, and Lestrade. His investigation into Moriarty's plans, post-mortem and otherwise, also drew him back to London.

The Fulmer murder investigation, however, was what made him stay in London longer than he planned. Sherlock knew it wasn't the best way to go about things. After all, Mycroft had run of all the cameras in London, and most of the Yard knew him by sight. He could hide himself among the Homeless Network and disguises his face, but between rain and wind, Sherlock's identity wouldn't remain hidden for longer than a few days, at best.

Before leaving the city indefinitely, Sherlock discovered Mycroft had dropped in unexpectedly on John, which was highly suspicious. Thus, Sherlock was forced to inspect his own flat.

John had packed away his old notes and all of Sherlock's scientific equipment. He searched through everything, being sure to put every page back exactly where it was.

Then he noticed something odd.

John had a specific packing style, highly organized, probably a byproduct of his military career. Yet the third box had an untidy arrangement of files, as if it was put together in a hurry. And there at the bottom was a new folder with freshly printed pages.

Sherlock was tempted to take the entire file, but he couldn't risk it being missed. So instead he snagged the thumb drive tacked inside the folder, hoping it was a full digital copy.

That's how Sherlock found himself on Curzon Street looking up 27 C for the flat of Indigo Kendall Berwyn. Police tape covered the door, but the crime scene had been cold for two days.

Sherlock slipped in without incident, and he saw that the police report was complete rubbish. "Signs of a struggle" would be an apt description only if one were observing from outer space. The flat had been overrun with violence: blood and hair and even a spare fingernail.

He started in the living room, which was clearly where the attack began. Blood was on the sofa, across the table, but it was like drips, maybe from a bloody nose. He followed the struggle, which was downright vicious, as it moved into the hall, as exhibited by knocked over pictures, and then to the kitchen and even the bathroom.

Sherlock pictured Indigo Kendall Berwyn as described in the report. She was approximately 1.6m tall and 72 kilos. Originally, he assumed she was heavyset, but now he reconsidered. Several impact points in the wall suggested a heel or a fist, but they were all small in diameter. Miss Berwyn was clearly trained in martial arts of some variety. Without a photo, Sherlock could only guess muscle mass and body structure, but 'fit' would be the right word. Very fit.

He turned his attention to the other party. From the heel imprint of the assailant's boot, the attacker was a male about 1.8m tall and weighing over 86 kilos. Whoever he was, he wasn't a skilled kidnapper or assassin, and he certainly wasn't ready for Miss Berwyn to put up a fight.

As this occurred to him, Sherlock returned to the living room. The disarray was not from the fight alone. Blood spattered over papers and tossed over clothing. Yes, the assailant came here to find something, either before or instead of abduction.

Sherlock retraced the steps, but the forensics team and the police had already been over the place, contaminating the scene with footprints and signs of moment. It was entirely possible the attacker removed something from the trunk in her bedroom as well as the locked drawer in her desk. Or it could be neither, depending on how tidy Miss Berwyn kept her flat.

He swept over the area. A woman who studied the martial arts was either interested in the sport or preparedness. Given her exhibited proficiency, Sherlock deducted it was the latter. If she prepared for an assault, then she would've dealt with other possible issues, including thieves. Which meant she had hiding places. Clever ones.

Sherlock remembered the living room, kitchen, and bedroom. They all had frequent use. Nothing out of place, nothing overused, so it must be concealed somewhere she frequents. He ran through the flat again and considered where the attacker didn't look...

None of the books on the shelf were touched, so he started there.

After about thirty minutes, Sherlock found three handmade hideaway books with bagged evidence concealed. At least, he assumed as much, since Miss Berwyn was a forensics expert.

Sherlock was considering this evidence when a throat cleared.

"Forty minutes? Really Sherlock, you're getting slow," a familiar voice said. "Perhaps you need a skull or Doctor John Watson. Or maybe being dead is a factor."

Sherlock turned to face his brother. "Mycroft."

"You must have expected this," Mycroft said.

"I was waiting for you to catch up," Sherlock replied slyly. "That thumb drive was you all over, wasn't it?"

"It took you twenty minutes to even look at the book shelves to begin with," Mycroft said. "Disgraceful."

"As you said, I haven't my skull or John," Sherlock said. "And being dead requires an element of silence so as to not attract attention."

"I won't ask how you managed to die without my help," Mycroft said softly. "But I will ask why you didn't bother telling me."

"I walked into your little Sherlock trap, that's as good as telling you."

"I mean before your death."

Sherlock scoffed. "You aren't really... you're not telling me that you cared?"

There was an excessively long pause that was simultaneously painful and profound. Somewhere in that moment, Sherlock received his answer, and the air of smugness sloughed off him.

Mycroft straightened his tie and adjusted the point of his umbrella before speaking. "Even you can't be foolish enough to assume I wouldn't care that you died."

Just like that, the moment passed, and the Holmes brothers were again themselves.

Sherlock said, "If a long speech about mother is coming, you can save it."

"Oh, no," Mycroft replied. "Because I won't be the one to tell her."

"You're just going to let her think I'm dead?" Sherlock asked indignantly.

Mycroft smiled. "Am I to assume correctly that you're looking into the women who cleared your name?"

"What?"

"Indigo Kendall Berwyn. She quite expediently cleared your name with exceptionally precise forensics," Mycroft said.

"That's too many adverbs," Sherlock said. "What do you know?"

"Have you heard of the Engineer?"

"Mycroft, I'm supposed to be dead, so the longer you take to impart information, the more likely I will become suddenly undead, which will be unhelpful in my plans."

"The Engineer has contacted John Watson," Mycroft said. "Most unusual."

"Miss Berwyn is this Engineer person, I presume?"

"We have dozens of names on file for this woman, and I highly doubt Indigo Kendall Berwyn is a legitimate name for anyone."

"Why did she contact John? Is... is he all right?"

"Yes, yes, he's fine," Mycroft dismissed. "She contacted him over the Fulmer case and you apparently. We don't know much about her. Occasionally, the Engineer will expose criminal activity. Never with credentials or as a witness, but evidence enough. It's troublesome, really. A different identity every time."

"So she picked a pseudonym to brand herself?"

"She's very particular about the people she contacts," Mycroft continued. "Her turning up at the Yard for over a week is unprecedented."

"And now someone has abducted her," Sherlock said.

"It appears so," Mycroft said. "Which means someone identified her before we did."

"You sound unhappy."

"Disturbed is more like it," Mycroft said.

"Fascinating," Sherlock said.

"Are you telling me that you're interested in investigating a case that I brought to your attention?" Mycroft asked.

"Just this once, for the novelty," Sherlock replied.